From ee4286d995c8e9169b92c4531013f7eed3751e39 Mon Sep 17 00:00:00 2001
From: Claus Jonathan Fritzemeier <clausjonathan.fritzemeier@hhu.de>
Date: Tue, 24 Oct 2017 15:24:27 +0200
Subject: [PATCH] writeSBML and NA values in attr fields
---
DESCRIPTION | 4 +--
R/sybilSBML.R | 72 ++++++++++++++++++++++++++++++++++++++++++++-------
inst/NEWS.Rd | 6 +++++
3 files changed, 70 insertions(+), 12 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index a46a8fa..b02d8a5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: sybilSBML
Type: Package
Title: SBML Integration in Package 'Sybil'
Version: 3.0.2
-Date: 2017-01-12
+Date: 2017-10-24
Authors@R: c(person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut", "ctb")),
person("Deya", "Alzoubi", role = "ctb"),
@@ -16,7 +16,7 @@ License: GPL-3 | file LICENSE
LazyLoad: yes
Collate: generics.R sbmlPtrClass.R sbmlErrorClass.R sybilSBML.R
uglyHack.R readSBMLmod.R zzz.R
-Packaged: 2017-01-12 07:11:55 UTC; jonathan
+Packaged: 2017-10-24 07:11:55 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
Deya Alzoubi [ctb],
diff --git a/R/sybilSBML.R b/R/sybilSBML.R
index b3eb40b..88abbc4 100644
--- a/R/sybilSBML.R
+++ b/R/sybilSBML.R
@@ -421,20 +421,63 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
### Start newSybil attr
if(newSybil)
{
- if(("notes" %in% colnames(mod_attr(morg))) && (printNotes) ) mod_notes<-as.character(mod_attr(morg)[['notes']])
- if(("annotation" %in% colnames(mod_attr(morg))) && (printAnnos) ) mod_annotation<-as.character(mod_attr(morg)[['annotation']])
+ if(("notes" %in% colnames(mod_attr(morg))) && (printNotes) ) {
+ mod_notes<-as.character(mod_attr(morg)[['notes']])
+ if(any(is.na(mod_notes))){
+ stop("mod_notes mustn't be NA")
+ }
+ }
+ if(("annotation" %in% colnames(mod_attr(morg))) && (printAnnos) ) {
+ mod_annotation<-as.character(mod_attr(morg)[['annotation']])
+ if(any(is.na(mod_annotation))){
+ stop("mod_annotation mustn't be NA")
+ }
+ }
- if(("notes" %in% colnames(comp_attr(morg))) && (printNotes) ) com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
- if(("annotation" %in% colnames(comp_attr(morg))) && (printAnnos) ) com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
+ if(("notes" %in% colnames(comp_attr(morg))) && (printNotes) ){
+ com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
+ if(any(is.na(com_notes))){
+ stop("com_notes mustn't be NA")
+ }
+ }
+ if(("annotation" %in% colnames(comp_attr(morg))) && (printAnnos) ){
+ com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
+ if(any(is.na(com_annotation))){
+ stop("com_annotation mustn't be NA")
+ }
+ }
- if("charge" %in% colnames(met_attr(morg))) met_charge<- as.integer(as.list((met_attr(morg)[['charge']])))
- if("chemicalFormula" %in% colnames(met_attr(morg))) met_formula<-as.character(as.list((met_attr(morg)[['chemicalFormula']])))
- if(("annotation" %in% colnames(met_attr(morg))) && (printAnnos)) met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
- if("boundaryCondition" %in% colnames(met_attr(morg))) met_bnd<-as.logical(as.list((met_attr(morg)[['boundaryCondition']])))
+ if("charge" %in% colnames(met_attr(morg))){
+ met_charge<- as.integer(as.list((met_attr(morg)[['charge']])))
+ if(any(is.na(met_charge))){
+ stop("met_charge mustn't be NA")
+ }
+ }
+ if("chemicalFormula" %in% colnames(met_attr(morg))){
+ met_formula<-as.character(as.list((met_attr(morg)[['chemicalFormula']])))
+ if(any(is.na(met_formula))){
+ stop("met_formula mustn't be NA")
+ }
+ }
+ if(("annotation" %in% colnames(met_attr(morg))) && (printAnnos)){
+ met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
+ if(any(is.na(mod_notes))){
+ stop("met_anno mustn't be NA")
+ }
+ }
+ if("boundaryCondition" %in% colnames(met_attr(morg))){
+ met_bnd<-as.logical(as.list((met_attr(morg)[['boundaryCondition']])))
+ if(any(is.na(met_bnd))){
+ stop("met_bnd mustn't be NA")
+ }
+ }
if(("notes" %in% colnames(met_attr(morg))) && (printNotes) )
{ # delete Formular and charge from notes to do
met_notes<-as.character(as.list((met_attr(morg)[['notes']])))
+ if(any(is.na(met_notes))){
+ stop("met_notes mustn't be NA")
+ }
if (!is.null(met_charge) || !is.null(met_formula))
{
for ( i in 1:met_num(morg))
@@ -478,12 +521,21 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
}
}
- if(("annotation" %in% colnames(react_attr(morg))) && (printAnnos)) react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
+ if(("annotation" %in% colnames(react_attr(morg))) && (printAnnos)){
+ react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
+ if(any(is.na(react_anno))){
+ stop("react_anno mustn't be NA")
+ }
+ }
# Merge Notes with "our" Notes and make sure gpr Rules from gpr
if(("notes" %in% colnames(react_attr(morg))) && (printNotes))
{
react_notes<-as.character(as.list((react_attr(morg)[['notes']])))
+ if(any(is.na(react_notes))){
+ stop("react_notes mustn't be NA")
+ }
+
# using
# SubSystem EXISTIERT nicht colnames(subSys(ec))
@@ -572,4 +624,4 @@ writeSBML<- function(morg=NULL,level=2,version=4,fbcLevel=0,filename="export.xml
}
else message(paste("Could not write file ",filename,"\n",sep=""), appendLF = FALSE);
return (success)
-}
\ No newline at end of file
+}
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 043c961..e90f8c5 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -5,6 +5,12 @@
\encoding{UTF-8}
\newcommand{\CRANpkg}{\href{https://cran.r-project.org/package=#1}{\pkg{#1}}}
+% ---------------------------------------------------------------------------- %
+\section{Changes in version 3.0.2 2017-10-24}{
+ \itemize{
+ \item Removed bug when trying to write models with NA in, e.g. \code{met_attr}.
+ }
+}
% ---------------------------------------------------------------------------- %
\section{Changes in version 3.0.1 2016-12-16}{
--
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