diff create_sqlite_db.R @ 21:e8291b9d129b draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty

--- a/create_sqlite_db.R	Thu May 31 09:12:15 2018 -0400
+++ b/create_sqlite_db.R	Thu May 31 11:26:26 2018 -0400
@@ -142,52 +142,18 @@
     if (is.null(pth)){
         return(0)
     }
-    index <- 0
-    chunkSize <- 5000
-    print(pth)
-    con <- file(description=pth,open="r")   
-    df <- read.table(con, nrows=chunkSize,  header = TRUE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
-    headers = colnames(df)
-    print(head(df))
-    write_to_table(df, db_con, name, FALSE, filter_Score, filter_Rank)
+    DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)
 
-    repeat {
-        index <- index + 1
-        print(paste('Processing rows:', index * chunkSize))
- 
-        if (nrow(df) != chunkSize){
-                print('Processed all files!')
-                break
-        }
-       
-        df <- read.table(con, nrows=chunkSize, skip=0, header = FALSE, sep='\t', stringsAsFactors = FALSE,  comment.char = "")
-        colnames(df) <- headers
-
-
-	write_to_table(df, db_con, name, TRUE, filter_Score, filter_Rank)
-
- 
-        break
-    }
-   close(con)
 
 }
 
-write_to_table <- function(df, db_con, name, append, filter_Score, filter_Rank){
+write_to_table <- function(df, db_con, name, append){
 
        df <- df[!df$UID=='UID',]
         print(filter_Score)
         print(filter_Rank)
         print('filter rank and score')
 
-        if (!is.na(filter_Score)){
-           df <- df[df$Score>=filter_Score,]
-        }      
-
-        if (!is.na(filter_Rank)){
-      
-            df <- df[df$Rank<=filter_Rank,]
-        }
 
         # get peakid, an scan id
         df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
@@ -243,8 +209,13 @@
 add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con, filter_Score=NA, filter_Rank=5)
 add_probmetab(opt$probmetab_result, con)
 
+if (is.null(xset)){
+  DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
+}else{
 
+  DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)
 
+}
 
 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
              'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',