1. RGMQL
  2. Commit 844be1d057e938ac68d16187d4a429fa90c9a081
Browse code

ipdated read_gmql

Simone authored on 15/04/2018 11:23:41
Showing 16 changed files
R/GRangesToGMQL.R
History View file @ 844be1d
... ... 
@@ -179,7 +179,7 @@ export_gmql <- function(samples, dir_out, is_gtf)
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         node_list <- c(fixed_element, columns)
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     }
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-    schema <- file.path(directory,"granges.schema")
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+    schema <- file.path(directory,"granges.xml")
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     root <- xml2::xml_new_root("gmqlSchemaCollection")
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     xml2::xml_attr(root,"name") <- "DatasetName_SCHEMAS"
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     xml2::xml_attr(root,"xmlns") <- "http://genomic.elet.polimi.it/entities"
R/gmql_materialize.R
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... ... 
@@ -250,6 +250,9 @@ gmql_take <- function(input_data, rows)
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         stop("no schema defined")
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     reg_data_frame <- as.data.frame(reg)
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+    if (!length(reg_data_frame)){
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+        return(GRangesList())
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+    }
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     list <- split(reg_data_frame, reg_data_frame[1])
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     seq_name <- c("seqname","start","end","strand",schema)
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R/gmql_read.R
History View file @ 844be1d
... ... 
@@ -83,10 +83,20 @@ read_gmql <- function(dataset, parser = "CustomParser", is_local = TRUE,
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         if(basename(dataset) !="files")
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             dataset <- file.path(dataset,"files")
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-        schema_XML <- list.files(dataset, pattern = "*.schema$",
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-                                    full.names = TRUE)
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-        if(!length(schema_XML))
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-            stop("schema must be present")
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+        schema_SCHEMA <- list.files(dataset, pattern = "*.schema$",
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+                                        full.names = TRUE)
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+
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+        xml_schema <- list.files(dataset, pattern = "*.xml$",
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+                                        full.names = TRUE)
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+        xml_schema = xml_schema[!basename(xml_schema) %in% c("web_profile.xml")]
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+
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+        if(!length(schema_SCHEMA) && !length(xml_schema))
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+            stop("schema not present")
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+
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+        if(!length(schema_SCHEMA))
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+            schema_XML <- xml_schema
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+        else
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+            schema_XML <- schema_SCHEMA
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         schema_matrix <- .jnull("java/lang/String")
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         url <- .jnull("java/lang/String")
inst/example/DATASET/files/dataset.schema
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rename from inst/example/DATASET/files/dataset.schema
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rename to inst/example/DATASET/files/dataset.xml
inst/example/DATASET_GDM/files/test.schema
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rename from inst/example/DATASET_GDM/files/test.schema
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rename to inst/example/DATASET_GDM/files/test.xml
inst/example/DATASET_META/files/test.schema
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similarity index 100%
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rename from inst/example/DATASET_META/files/test.schema
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rename to inst/example/DATASET_META/files/test.xml
inst/example/EXON/files/test.schema
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similarity index 100%
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rename from inst/example/EXON/files/test.schema
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rename to inst/example/EXON/files/test.xml
inst/example/MUT/files/test.schema
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similarity index 100%
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rename from inst/example/MUT/files/test.schema
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rename to inst/example/MUT/files/test.xml
inst/example/TEAD/files/job_TEAD_HM_TF_ECC1_PROMonly.schema
History View file @ 844be1d
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similarity index 100%
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rename from inst/example/TEAD/files/job_TEAD_HM_TF_ECC1_PROMonly.schema
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rename to inst/example/TEAD/files/job_TEAD_HM_TF_ECC1_PROMonly.xml
inst/example/TF_TEAD/files/schema.schema
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similarity index 100%
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rename from inst/example/TF_TEAD/files/schema.schema
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rename to inst/example/TF_TEAD/files/schema.xml
inst/example/files/S_1.gtf
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deleted file mode 100644
... ... 
@@ -1,574 +0,0 @@
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-##source-version rtracklayer 1.36.6
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-##date 2018-02-20
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-chr7	rtracklayer	sequence_feature	128612480	128612636	0	-	.	name "NM_001191028"
572 
-chr7	rtracklayer	sequence_feature	128612480	128612636	0	-	.	name "NM_012470"
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-chr7	rtracklayer	sequence_feature	128614922	128615016	0	-	.	name "NR_034053"
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-chr7	rtracklayer	sequence_feature	128614922	128615016	0	-	.	name "NM_001191028"
inst/example/files/S_1.gtf.meta
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-annotation_type	exons
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-assembly	hg19
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-name	RefSeqGeneExons
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-original_provider	RefSeq
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-provider	POLIMI
inst/example/files/granges.schema
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-<?xml version="1.0" encoding="UTF-8"?>
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-<gmqlSchemaCollection xmlns="http://genomic.elet.polimi.it/entities" name="DatasetName_SCHEMAS" type="gtf" coordinate_system="1-based">
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-  <gmqlSchema>
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-    <field type="STRING">seqname</field>
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-    <field type="STRING">source</field>
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-    <field type="STRING">feature</field>
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-    <field type="LONG">start</field>
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-    <field type="LONG">end</field>
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-    <field type="DOUBLE">score</field>
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-    <field type="STRING">strand</field>
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-    <field type="STRING">frame</field>
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-    <field type="STRING">name</field>
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-  </gmqlSchema>
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-</gmqlSchemaCollection>
vignettes/.build.timestamp
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vignettes/RGMQL-vignette.R
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+## ---- initialization-----------------------------------------------------
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+library('RGMQL')
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+
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+## ---- initialization_RGMQLlib--------------------------------------------
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+library('RGMQLlib')
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+
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+## ---- init---------------------------------------------------------------
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+init_gmql()
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+
vignettes/RGMQL-vignette.Rmd
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@@ -385,7 +385,7 @@ After the execution, the context of scalable data management engine is stopped
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 and a new invocation of *init_gmql()* is needed.
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 Beside *execute()* we can use:
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-```{r, take}
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+```{r, take,eval=FALSE}
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 g <- take(exon_res, rows = 45)
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 ```
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 to execute all *collect()* commands in the RGMQL query and extract data
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@@ -563,7 +563,7 @@ exon_res = arrange(exon3, list(DESC("exon_count")))
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 ```
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 ```{r, remote materialize, eval = FALSE}
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-collect(exon_res)
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+collect(exon_res,"exon_res")
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 ```
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 ```{r, remote execute, eval = FALSE}
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@@ -653,7 +653,7 @@ exon_res = arrange(exon3, list(DESC("exon_count")))
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 Materialize result:
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 ```{r, mixed materialize, eval = FALSE}
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-collect(exon_res)
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+collect(exon_res,"exon_res")
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 ```
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 Execute processing: