# HG changeset patch
# User mingchen0919
# Date 1521602354 14400
# Node ID a00a424ff951c1f8a09df2ca041110939bad8dee
# Parent  f8ac93c417209612370cf2d069ce9f50b2cff4b3
add r-httr package

diff -r f8ac93c41720 -r a00a424ff951 variant_simple_search.Rmd
--- a/variant_simple_search.Rmd	Tue Mar 20 13:59:04 2018 -0400
+++ b/variant_simple_search.Rmd	Tue Mar 20 23:19:14 2018 -0400
@@ -1,12 +1,9 @@
 ---
-title: 'HTML report title'
+title: 'myvariant.info: simple search'
 output:
     html_document:
-      number_sections: true
-      toc: true
       theme: cosmo
       highlight: tango
-      code_folding: hide
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
@@ -23,5 +20,19 @@
 opt
 ```
 
+```{r}
+req = POST('http://myvariant.info/v1/variant?',
+           add_headers(
+             'accept' = "application/json",
+             'Content-Type' = "application/x-www-form-urlencoded"
+           ),
+           body = list(ids = opt$X_q, dotfield = 'true'), encode = 'form')
 
 
+json = content(req, as = 'text')
+df = t(as.data.frame(fromJSON(json)))
+colnames(df) = strsplit(ids, ',')[[1]]
+datatable(df)
+```
+
+
diff -r f8ac93c41720 -r a00a424ff951 variant_simple_search.xml
--- a/variant_simple_search.xml	Tue Mar 20 13:59:04 2018 -0400
+++ b/variant_simple_search.xml	Tue Mar 20 23:19:14 2018 -0400
@@ -10,6 +10,7 @@
         <requirement type="package" version="0.2">r-dt</requirement>
         <requirement type="package" version="3.1">r-curl</requirement>
         <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
+        <requirement type="package" version="1.3.1">r-httr</requirement>
     </requirements>
     <macros>
         <import>mygene_and_myvariant_macros.xml</import>
@@ -23,11 +24,11 @@
 
         Rscript '${__tool_directory__}/variant_simple_search_render.R'
 
-			-o $report
-			-d $report.files_path
-			-s $sink_message
-			-q $variant_query
-			-f $return_fields
+			-o '$report'
+			-d '$report.files_path'
+			-s '$sink_message'
+			-q '$variant_query'
+			-f '$return_fields'
 
 
         
@@ -35,13 +36,11 @@
     <inputs>
         <param type="text" name="variant_query" label="Search keywords" optional="False">
             <sanitizer>
-                <valid initial="default">
-                    <add preset="string.printable"/>
-                </valid>
+                <valid initial="string.printable"/>
             </sanitizer>
         </param>
         <param type="select" name="return_fields" label="Returned fields" optional="False" multiple="True">
-            <expand macro="fields" />
+            <expand macro="fields"/>
         </param>
     </inputs>
     <outputs>
diff -r f8ac93c41720 -r a00a424ff951 variant_simple_search_render.R
--- a/variant_simple_search_render.R	Tue Mar 20 13:59:04 2018 -0400
+++ b/variant_simple_search_render.R	Tue Mar 20 23:19:14 2018 -0400
@@ -12,6 +12,7 @@
 library(rmarkdown)
 library(jsonlite)
 library(DT)
+library(httr)
 #------------------------------------------------