diff make_eml.R @ 1:3b0fa963ae3e draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline commit f00c48e2a16ba6154e6c1aa50330586eefb13a32

--- a/make_eml.R	Mon Dec 04 21:48:55 2023 +0000
+++ b/make_eml.R	Sat Dec 23 20:41:26 2023 +0000
@@ -1,5 +1,5 @@
 ##07/06/2023 ##Genthon Tanguy
-##update 15/11/2023 ##Seguineau Pauline
+##update 15/11/2023 ## Seguineau Pauline
 
 ###make_eml
 
@@ -9,17 +9,27 @@
   start <- args[2]
   end <-args[3]
   data_table <- args[4]
-  data_other <- args[5]
-  destable <- args[6]
-  desother <- args[7]
-  quote <- args[8]
-  table_url <- args[9]
-  other_url <- args[10]
+  data_raster <- args[5]
+  data_vector <- args[6]
+  data_other <- args[7]
+  destable <- args[8]
+  desraster<- args[9]
+  desvector<- args[10]
+  desother <- args[11]
+  quote <- args[12]
+  table_url <- args[13]
+  other_url <- args[14]
+  raster_url <- args[15]
+  vector_url <- args[16]
 }
- 
+
+#Load package
+
+library(EMLassemblyline)
+sessionInfo()
+
 
 ###Format data###
-
 if (data_table == ""){
     table=NULL
 }else{
@@ -48,6 +58,22 @@
 }
 
   
+if (data_raster == ""){
+    raster=NULL
+}else{
+    raster =  strsplit(data_raster," ")
+    for (file in raster){
+         name_raster = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+    
+if (data_vector == ""){
+    vector=NULL
+}else{
+    vector =  strsplit(data_vector," ")
+    for (file in vector){
+         name_vector = gsub("\\.[a-zA-Z]*", "", file)}
+    }
+
 if (data_other == ""){
     other=NULL
 }else{
@@ -63,6 +89,19 @@
        des_table =  strsplit(destable,",")}
 }
 
+if (data_raster !=""){
+   if (desraster == ""){
+       des_raster = name_raster
+   }else{
+       des_raster =  strsplit(desraster,",")}
+}
+
+if (data_vector !=""){ 
+   if (desvector == ""){
+       des_vector = name_vector
+   }else{
+       des_vector =  strsplit(desvector,",")}
+}
 
 if (data_other !=""){
    if (desother == ""){
@@ -71,7 +110,6 @@
        des_other =  strsplit(desother,",")}
 }
 
-
 if (data_table !=""){
    if (table_url == ""){
        urltable = ""
@@ -90,9 +128,79 @@
    }
 }
 
+if (data_raster !=""){
+   if (raster_url == ""){
+       urlraster = ""
+   }else{
+       raster_url = gsub("\\-" ,"", raster_url)
+       urlraster =  strsplit(raster_url,",")
+   }
+}
+
+if (data_vector !=""){
+   if (vector_url == ""){
+       urlvector = ""
+   }else{
+       vector_url = gsub("\\-" ,"", vector_url)
+       urlvector =  strsplit(vector_url,",")
+   }
+}
+
+
+
 ###Make EML###
    
-if (!is.null(table) && !is.null(other)){
+if (!is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end))
+   
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]]
+                      )
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
    
    EMLassemblyline::make_eml(
                       path="output_template",
@@ -105,22 +213,203 @@
                       data.table.description = des_table[[1]],
                       data.table.quote.character = tablequote,
                       data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (!is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+  
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]])
+                      
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && is.null(other)){
+   
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (is.null(table) && !is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                 
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+                      
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]])
+
+}else if (!is.null(table) && is.null(raster) && is.null(vector) && !is.null(other)){
+
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
                       other.entity=other[[1]],
                       other.entity.name = name_other,
                       other.entity.description = des_other[[1]],
-                      other.entity.url= urlother[[1]]
-                      )
-                      
-}else if (is.null(table) && is.null(other)){
-  
+                      other.entity.url= urlother[[1]])
+
+}else if (is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
+
    EMLassemblyline::make_eml(
                       path="output_template",
                       data.path="data_files",
                       eml.path=".", 
                       dataset.title = title,
-                      temporal.coverage = c(start,end))
+                      temporal.coverage = c(start,end),
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && is.null(raster) && !is.null(vector) && !is.null(other)){
    
-}else if (!is.null(table) && is.null(other)){
+   EMLassemblyline::make_eml(
+                      path="output_template",
+                      data.path="data_files",
+                      eml.path=".", 
+                      dataset.title = title,
+                      temporal.coverage = c(start,end),
+                      data.table=table[[1]],
+                      data.table.name = name_table,
+                      data.table.description = des_table[[1]],
+                      data.table.quote.character = tablequote,
+                      data.table.url = urltable[[1]],
+                      spatial.vector=vector[[1]],
+                      spatial.vector.name = name_vector,
+                      spatial.vector.description = des_vector[[1]],
+                      spatial.vector.url = urlvector[[1]],
+                      other.entity=other[[1]],
+                      other.entity.name = name_other,
+                      other.entity.description = des_other[[1]],
+                      other.entity.url= urlother[[1]])
+
+}else if (!is.null(table) && !is.null(raster) && is.null(vector) && !is.null(other)){
 
    EMLassemblyline::make_eml(
                       path="output_template",
@@ -132,26 +421,18 @@
                       data.table.name = name_table,
                       data.table.description = des_table[[1]],
                       data.table.quote.character = tablequote,
-                      data.table.url = urltable[[1]])
-                      
-
-}else if (is.null(table) && !is.null(other)){
-
-   EMLassemblyline::make_eml(
-                      path="output_template",
-                      data.path="data_files",
-                      eml.path=".", 
-                      dataset.title = title,
-                      temporal.coverage = c(start,end),
+                      data.table.url = urltable[[1]],
+                      spatial.raster=raster[[1]],
+                      spatial.raster.name = name_raster,
+                      spatial.raster.description = des_raster[[1]],
+                      spatial.raster.url = urlraster[[1]],
                       other.entity=other[[1]],
                       other.entity.name = name_other,
                       other.entity.description = des_other[[1]],
                       other.entity.url= urlother[[1]])}
-                      
 
-
+issues()
 old.names <- list.files(path=".", pattern=".xml")
-print(old.names)
 file.rename(from=old.names, to="eml.xml")