Simone authored on 18/05/2021 20:04:54
Simone authored on 27/03/2021 15:11:43
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@@ -41,6 +41,21 @@ a new dataset is created on remote repository |
| 41 | 41 |
\details{
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If no error occurs, it prints "Upload Complete", otherwise a specific error |
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is printed |
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+ |
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+NOTE: |
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+The folder layout must obey the following rules and adopt |
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+the following layout: |
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+The dataset folder can have any name, but must contains the |
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+sub-folders named: "files". |
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+The sub-folder "files" contains the dataset files and |
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+the schema xml file. |
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+The schema files adopt the following the naming conventions: |
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+ |
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+- "schema.xml" |
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+- "test.schema" |
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+ |
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+The names must be in LOWERCASE. Any other schema file |
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+will not be conisdered, if both are present, "test.schema" will be used. |
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} |
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\examples{
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| 46 | 61 |
|
Simone authored on 21/03/2021 14:34:30
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old mode 100644 |
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new mode 100755 |
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@@ -4,7 +4,7 @@ |
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\alias{upload_dataset}
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\title{Upload dataset}
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\usage{
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-upload_dataset(url, datasetName, folderPath, schemaName = NULL, isGMQL = TRUE) |
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+upload_dataset(url, datasetName, folderPath, schemaName = NULL) |
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| 8 | 8 |
} |
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\arguments{
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\item{url}{string url of server: It must contain the server address
|
Simone authored on 09/02/2021 09:07:32
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@@ -4,8 +4,7 @@ |
| 4 | 4 |
\alias{upload_dataset}
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\title{Upload dataset}
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\usage{
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-upload_dataset(url, datasetName, folderPath, schemaName = NULL, |
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- isGMQL = TRUE) |
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+upload_dataset(url, datasetName, folderPath, schemaName = NULL, isGMQL = TRUE) |
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| 9 | 8 |
} |
| 10 | 9 |
\arguments{
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\item{url}{string url of server: It must contain the server address
|
Simone authored on 16/08/2018 09:03:55
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@@ -54,7 +54,7 @@ test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
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## Login to GMQL REST services suite at remote url |
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-remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/" |
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+remote_url <- "http://www.gmql.eu/gmql-rest/" |
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| 58 | 58 |
login_gmql(remote_url) |
| 59 | 59 |
|
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## Upload of GMQL dataset with "dataset1" as name, without specifying any |
Simone authored on 19/01/2018 11:06:58
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@@ -25,7 +25,7 @@ schemaName available are: |
| 25 | 25 |
\item{BED}
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\item{BEDGRAPH}
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} |
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-if schemaName is NULL it's looking for a XML schema file to read in the |
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+if schemaName is NULL, it looks for a XML schema file to read in the |
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folderPath} |
| 30 | 30 |
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\item{isGMQL}{logical value indicating whether it is uploaded a GMQL
|
| ... | ... |
@@ -52,12 +52,12 @@ is printed |
| 52 | 52 |
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test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
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-## login to GMQL REST services suite at remote url |
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+## Login to GMQL REST services suite at remote url |
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remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/" |
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login_gmql(remote_url) |
| 59 | 59 |
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-## upload of GMQL dataset with "dataset1" as name without specifying any |
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+## Upload of GMQL dataset with "dataset1" as name, without specifying any |
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## schema |
| 62 | 62 |
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upload_dataset(remote_url, "dataset1", folderPath = test_path) |
Simone authored on 11/01/2018 13:10:15
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@@ -25,7 +25,8 @@ schemaName available are: |
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\item{BED}
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\item{BEDGRAPH}
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} |
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-if schemaName is NULL it's looking for a XML schema file to read} |
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+if schemaName is NULL it's looking for a XML schema file to read in the |
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+folderPath} |
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| 29 | 30 |
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\item{isGMQL}{logical value indicating whether it is uploaded a GMQL
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dataset or not} |
Simone authored on 10/12/2017 16:29:05
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@@ -11,11 +11,12 @@ upload_dataset(url, datasetName, folderPath, schemaName = NULL, |
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\item{url}{string url of server: It must contain the server address
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and base url; service name is added automatically} |
| 13 | 13 |
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-\item{datasetName}{name of dataset to get}
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+\item{datasetName}{name of dataset to create in repository}
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| 15 | 15 |
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-\item{folderPath}{string local path to the folder containing the samples}
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+\item{folderPath}{string local path to the folder containing the samples
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+files} |
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| 17 | 18 |
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-\item{schemaName}{string name of schema used to parse the samples
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+\item{schemaName}{string name of schema used to parse the samples;
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schemaName available are: |
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\itemize{
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\item{NARROWPEAK}
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| ... | ... |
@@ -24,9 +25,10 @@ schemaName available are: |
| 24 | 25 |
\item{BED}
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\item{BEDGRAPH}
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} |
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-if schema is NULL it's looking for a XML schema file to read} |
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+if schemaName is NULL it's looking for a XML schema file to read} |
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| 28 | 29 |
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-\item{isGMQL}{logical value indicating whether is GMQL dataset or not}
|
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+\item{isGMQL}{logical value indicating whether it is uploaded a GMQL
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+dataset or not} |
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} |
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\value{
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None |
| ... | ... |
@@ -34,20 +36,30 @@ None |
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\description{
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It uploads a folder (GMQL or not) containing sample files using |
| 36 | 38 |
the proper GMQL web service available on a remote server: |
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-a new dataset is created on repository |
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+a new dataset is created on remote repository |
|
| 38 | 40 |
} |
| 39 | 41 |
\details{
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-If no error occures print "Upload Complete", otherwise a specific error |
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+If no error occurs, it prints "Upload Complete", otherwise a specific error |
|
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is printed |
| 42 | 44 |
} |
| 43 | 45 |
\examples{
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| 44 | 46 |
|
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\dontrun{
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-### upload of GMQL dataset with no schema selection |
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+## This statement defines the path to the folder "DATASET_GDM" in the |
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+## subdirectory "example" of the package "RGMQL" |
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+ |
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test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
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-remote_url <- "http://genomic.elet.polimi.it/gmql-rest-r/" |
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+ |
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+## login to GMQL REST services suite at remote url |
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+ |
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+remote_url <- "http://genomic.deib.polimi.it/gmql-rest-r/" |
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login_gmql(remote_url) |
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+ |
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+## upload of GMQL dataset with "dataset1" as name without specifying any |
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+## schema |
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+ |
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upload_dataset(remote_url, "dataset1", folderPath = test_path) |
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+ |
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} |
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} |
Simone authored on 21/11/2017 13:43:55
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@@ -1,5 +1,5 @@ |
| 1 | 1 |
% Generated by roxygen2: do not edit by hand |
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-% Please edit documentation in R/datasetOp.R |
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+% Please edit documentation in R/web-services.R |
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\name{upload_dataset}
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\alias{upload_dataset}
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\title{Upload dataset}
|
| ... | ... |
@@ -46,9 +46,8 @@ is printed |
| 46 | 46 |
|
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### upload of GMQL dataset with no schema selection |
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test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
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-remote_url <- "http://130.186.13.219/gmql-rest" |
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+remote_url <- "http://genomic.elet.polimi.it/gmql-rest-r/" |
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login_gmql(remote_url) |
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upload_dataset(remote_url, "dataset1", folderPath = test_path) |
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} |
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- |
|
| 54 | 53 |
} |
Simone authored on 14/11/2017 15:58:33
Simone authored on 10/11/2017 09:12:05
Simone authored on 08/11/2017 13:30:29
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new file mode 100644 |
| ... | ... |
@@ -0,0 +1,54 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/datasetOp.R |
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+\name{upload_dataset}
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+\alias{upload_dataset}
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+\title{Upload dataset}
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+\usage{
|
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+upload_dataset(url, datasetName, folderPath, schemaName = NULL, |
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+ isGMQL = TRUE) |
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+} |
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+\arguments{
|
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+\item{url}{string url of server: It must contain the server address
|
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+and base url; service name is added automatically} |
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+ |
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+\item{datasetName}{name of dataset to get}
|
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+ |
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+\item{folderPath}{string local path to the folder containing the samples}
|
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+ |
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+\item{schemaName}{string name of schema used to parse the samples
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+schemaName available are: |
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+\itemize{
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+\item{NARROWPEAK}
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+\item{BROADPEAK}
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+\item{VCF}
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+\item{BED}
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+\item{BEDGRAPH}
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+} |
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+if schema is NULL it's looking for a XML schema file to read} |
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+ |
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+\item{isGMQL}{logical value indicating whether is GMQL dataset or not}
|
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+} |
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+\value{
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+None |
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+} |
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+\description{
|
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+It uploads a folder (GMQL or not) containing sample files using |
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+the proper GMQL web service available on a remote server: |
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+a new dataset is created on repository |
|
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+} |
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+\details{
|
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+If no error occures print "Upload Complete", otherwise a specific error |
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+is printed |
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+} |
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+\examples{
|
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+ |
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+\dontrun{
|
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+ |
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+### upload of GMQL dataset with no schema selection |
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+test_path <- system.file("example", "DATASET_GDM", package = "RGMQL")
|
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+remote_url <- "http://130.186.13.219/gmql-rest" |
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+login_gmql(remote_url) |
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+upload_dataset(remote_url, "dataset1", folderPath = test_path) |
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+} |
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+ |
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+} |