1. RGMQL
  2. Commit 0ad65e7f4716ae8ed9e7fbaecd7a6f22d99c4d53
Browse code

minor fix

Simone authored on 24/12/2017 11:42:33
Showing 14 changed files
R/S3Operator.R
History View file @ 0ad65e7
... ... 
@@ -118,8 +118,7 @@ check.META <- function(type)
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 {
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     check.OPERATOR(value)
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     value <- toupper(value)
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-    if(!identical(value,"DOUBLE") && !identical(value,"INTEGER") &&
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-            !identical(value,"STRING"))
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+    if(!value %in% c("DOUBLE","INTEGER","STRING"))
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         stop("only DOUBLE or INTEGER or STRING")
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 }
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... ... 
@@ -143,7 +142,7 @@ check.NIL <- function(value)
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 {
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     check.OPERATOR(value)
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     value <- toupper(value)
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-    if(!identical(value,"DOUBLE") && !identical(value,"INTEGER"))
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+    if(!value %in% c("DOUBLE","INTEGER"))
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         stop("only DOUBLE or INTEGER")
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 }
R/Utils.R
History View file @ 0ad65e7
... ... 
@@ -65,15 +65,15 @@
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 .join_condition <- function(cond)
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 {
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     cond_matrix <- NULL
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-    def <- cond$def
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+    def <- cond$condition$def
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     if(!is.null(def))
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         cond_matrix <- rbind(cond_matrix, def)
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-    exact <- cond$exact
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+    exact <- cond$condition$exact
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     if(!is.null(exact))
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         cond_matrix <- rbind(cond_matrix, exact)
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-    full <- cond$full
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+    full <- cond$condition$full
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     if(!is.null(full))
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         cond_matrix <- rbind(cond_matrix, full)
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     cond_matrix
R/filter-extract-function.R
History View file @ 0ad65e7
... ... 
@@ -256,10 +256,10 @@ filter_and_extract <- function(data, metadata = NULL,
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         df_only_regions <- dplyr::bind_cols(df_list)
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         complete_df <- dplyr::bind_cols(df,df_only_regions)
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-        region_names <- names(complete_df)[-(1:4)]
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+        region_names <- names(complete_df)[-(seq_len(4))]
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         region_names <- gsub('[0-9]+', '',region_names)
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         region_names <- paste(region_names,suffixes,sep = ".")
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-        region_names <- c(names(complete_df)[(1:4)],region_names )
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+        region_names <- c(names(complete_df)[(seq_len(4))],region_names )
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         names(complete_df) <- region_names
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         g <- GenomicRanges::makeGRangesFromDataFrame(complete_df,
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                             keep.extra.columns = TRUE,
R/gmql_cover.R
History View file @ 0ad65e7
... ... 
@@ -192,7 +192,7 @@ gmql_cover <- function(input_data, min_acc, max_acc, groupBy, aggregates, flag)
192 192
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 .check_cover_param <- function(param, is_min)
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 {
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-    if(length(param))
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+    if(length(param) > 1)
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         stop("length > 1")
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     if(is.numeric(param))
R/gmql_group.R
History View file @ 0ad65e7
... ... 
@@ -106,7 +106,7 @@ gmql_group <- function(input_data, group_meta, group_reg, region_aggregates,
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         if(!length(group_reg))
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             group_reg <- .jnull("java/lang/String")
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-        group_reg <- .jarray(metadata)
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+        group_reg <- .jarray(group_reg)
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     }
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     else
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         group_reg <- .jnull("java/lang/String")
R/gmql_join.R
History View file @ 0ad65e7
... ... 
@@ -26,7 +26,7 @@
26 26 
 #'
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 #' @param joinBy \code{\link{condition_evaluation}} function to support
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 #' methods with groupBy or JoinBy input paramter
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-#'
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+#' @param reg_attr vector of string made up by schema field attribute
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 #' @param region_output single string that declares which region is given in
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 #' output for each input pair of left dataset and right dataset regions
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 #' satisfying the genometric predicate:
... ... 
@@ -81,17 +81,17 @@
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 #' @export
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 setMethod("merge", c("GMQLDataset","GMQLDataset"),
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                 function(x, y, genometric_predicate = NULL,
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-                    region_output = "CAT", joinBy = NULL)
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+                    region_output = "CAT", joinBy = NULL, reg_attr = NULL)
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                 {
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                     ptr_data_x <- value(x)
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                     ptr_data_y <- value(y)
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                     gmql_join(ptr_data_x, ptr_data_y, genometric_predicate,
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-                                joinBy, region_output)
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+                                joinBy, region_output, reg_attr)
90 90 
                 })
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 gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,
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-                            region_output)
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+                            region_output, reg_attributes)
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 {
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     if(!is.null(genometric_predicate))
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     {
... ... 
@@ -125,6 +125,22 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,
125 125 
     else
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         join_matrix <- .jnull("java/lang/String")
127 127
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+    if(!is.null(reg_attributes))
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+    {
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+        if(!is.character(reg_attributes))
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+            stop("metadata: no valid input")
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+
133 
+        reg_attributes <- reg_attributes[!reg_attributes %in% ""]
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+        reg_attributes <- reg_attributes[!duplicated(reg_attributes)]
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+
136 
+        if(!length(reg_attributes))
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+            reg_attributes <- .jnull("java/lang/String")
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+
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+        reg_attributes <- .jarray(reg_attributes)
140 
+    }
141 
+    else
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+        reg_attributes <- .jnull("java/lang/String")
143 
+
128 144 
     ouput <- toupper(region_output)
129 145 
     if(!ouput %in% c("CAT", "LEFT", "RIGHT", "INT", "BOTH", "RIGHT_DIST",
130 146 
                         "LEFT_DIST"))
... ... 
@@ -132,8 +148,8 @@ gmql_join <- function(left_data, right_data, genometric_predicate, joinBy,
132 148 
                 or int (intersection)")
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     WrappeR <- J("it/polimi/genomics/r/Wrapper")
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-    response <- WrappeR$join(genomatrix, join_matrix, ouput, left_data,
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-                                right_data)
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+    response <- WrappeR$join(genomatrix, join_matrix, ouput,reg_attributes,
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+                                left_data, right_data)
137 153 
     error <- strtoi(response[1])
138 154 
     val <- response[2]
139 155 
     if(error!=0)
R/gmql_select.R
History View file @ 0ad65e7
... ... 
@@ -1,7 +1,7 @@
1 1 
 filter.GMQLDateset <- function(.data, m_predicate = NULL, r_predicate = NULL,
2 2 
                                     semijoin = NULL)
3 3 
 {
4 
-    val <- .data@value
4 
+    val <- value(.data)
5 5 
     meta_pred <- substitute(m_predicate)
6 6 
     if(!is.null(meta_pred))
7 7 
     {
R/web-services.R
History View file @ 0ad65e7
... ... 
@@ -843,11 +843,8 @@ upload_dataset <- function(url, datasetName, folderPath, schemaName = NULL,
843 843 
         }
844 844 
         else
845 845 
         {
846 
-            if(!identical(schema_name,"narrowpeak") &&
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-                !identical(schema_name,"vcf") &&
848 
-                !identical(schema_name,"broadpeak") &&
849 
-                !identical(schema_name,"bed")  &&
850 
-                !identical(schema_name,"bedgraph"))
846 
+            if(!schema_name %in% c("narrowpeak","vcf","broadpeak","bed",
847 
+                                    "bedgraph"))
851 848 
                 stop("schema not admissable")
852 849
853 850 
             URL <- paste0(real_URL,"datasets/",datasetName,
inst/example/TF_TEAD/files/S_00000.gdm
History View file @ 0ad65e7
854 851 
new file mode 100755
... ... 
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1133 
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1134 
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1135 
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1136 
+chr1	151519590	151519792	*	.	1000	210.7676284	-1	4.49710941	106
1137 
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1138 
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1139 
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1140 
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1141 
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1142 
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1143 
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1144 
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1145 
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1146 
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1147 
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1148 
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1149 
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1150 
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1151 
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1152 
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1153 
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1154 
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1155 
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1156 
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1157 
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1158 
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1159 
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1160 
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1161 
+chr1	154580154	154580404	*	.	341	53.42072839	-1	4.49710941	125
1162 
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1163 
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1164 
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1165 
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1166 
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1167 
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1168 
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1169 
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1170 
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1171 
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1172 
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1173 
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1174 
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1175 
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1176 
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1177 
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1178 
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1179 
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1180 
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1181 
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1182 
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1183 
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1184 
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1185 
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1186 
+chr1	156076624	156076766	*	.	1000	164.28373356	-1	4.49710941	58
1187 
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1188 
+chr1	156093042	156093292	*	.	285	44.63505948	-1	4.49710941	125
1189 
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1190 
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1191 
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1192 
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1193 
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1194 
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