R/internal_string_to_df_inner_inner.R

In grishagin/RIGconvertbiopax: Convert BioPAX into Flat File and Back

######################################## internal_string_to_df_inner_inner ########################################
internal_string_to_df_inner_inner<-
    function(string
             ,el_id=""
             ,pav=""
             ,prop_vect){
        require(stringr)
        pattern = "([[:alpha:]]*?)=(.*?)\\{class=(.*?)\\}"
        #search for a given pattern in the string
        
        dFrame<-
            string %>%
            stringr::str_match_all(pattern) %>%
            .[[1]] %>%
            as.data.frame
        
        #if resultant dFrame does not have rows, return null
        if(nrow(dFrame)<1){
            return(NULL)
        }
        
        #... and take only pertaining columns of the hits
        #these numbers are hard-coded due to the pattern is known 
        #and expected to be one and only
        dFrame<-dFrame[,c(2:4)]
        
        #again, pattern is known and that's what it is
        colnames(dFrame)<-
            c("property"
              ,"property_value"
              ,"class")
        
        #exclude all NA values
        dFrame[dFrame=="NA"]<-NA
        dFrame<-
            dFrame %>% 
            filter(!is.na(property_value))
        
        #if resultant dFrame does not have rows, return null
        if(nrow(dFrame)<1){
            return(NULL)
        }
        
        #if it's a string with xrefs -- add corresponding 
        #joining lines (see below) and change ids accordingly
        #to account for appropriate id nesting
        if ("modificationType" %in% prop_vect & 
           "xref" %in% prop_vect){
            #"feature_modificationType_xref"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"ModificationFeature"
                                   ,"SequenceModificationVocabulary")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_fe")
                                 ,paste0(pav
                                         ,"_femo"))
                           ,property=c("feature"
                                       ,"modificationType"
                                       ,"xref")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_fe")
                                                  ,paste0(pav
                                                          ,"_femo")
                                                  ,paste0(pav
                                                          ,"_femoxr"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_femoxr")
        
        } else if ("modificationType" %in% prop_vect){
            #"feature_modificationType"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"ModificationFeature")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_fe"))
                           ,property=c("feature"
                                       ,"modificationType")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_fe")
                                                  ,paste0(pav
                                                          ,"_femo"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_femo")
            
        } else if ("sequenceIntervalBegin" %in% prop_vect){
            #"feature_featureLocation_sequenceIntervalBegin"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"FragmentFeature"
                                   ,"SequenceInterval")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_fe")
                                 ,paste0(pav
                                         ,"_fefe"))
                           ,property=c("feature"
                                       ,"featureLocation"
                                       ,"sequenceIntervalBegin")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_fe")
                                                  ,paste0(pav
                                                          ,"_fefe")
                                                  ,paste0(pav
                                                          ,"_fefeseb"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_fefeseb")
            
        } else if ("sequenceIntervalEnd" %in% prop_vect){
            #"feature_featureLocation_sequenceIntervalEnd"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"FragmentFeature"
                                   ,"SequenceInterval")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_fe")
                                 ,paste0(pav
                                         ,"_fefe"))
                           ,property=c("feature"
                                       ,"featureLocation"
                                       ,"sequenceIntervalEnd")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_fe")
                                                  ,paste0(pav
                                                          ,"_fefe")
                                                  ,paste0(pav
                                                          ,"_fefesee"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_fefesee")
            
        } else if ("featureLocation" %in% prop_vect){
            #"feature_featureLocation"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"FragmentFeature")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_fe"))
                           ,property=c("feature"
                                       ,"featureLocation")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_fe")
                                                  ,paste0(pav
                                                          ,"_fefe"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_fefe")
            
        } else if ("cellularLocation" %in% prop_vect &
                   "xref" %in% prop_vect){
            #"cellularLocation_xref"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,"CellularLocationVocabulary")
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_ce"))
                           ,property=c("cellularLocation"
                                       ,"xref")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_ce")
                                                  ,paste0(pav
                                                          ,"_cexr"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_cexr")
            
        } else if ("cellularLocation" %in% prop_vect){
            #"cellularLocation"
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER"))
                           ,id=c(el_id)
                           ,property=c("cellularLocation")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_ce"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_ce")
            
        } else if ("entityReference" %in% prop_vect){
            #since the class to which the xref belongs is not known
            #use a PLACEHOLDER instead
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER")
                                   ,paste0(el_id
                                           ,"PLACEHOLDERReference"))
                           ,id=c(el_id
                                 ,paste0(pav
                                         ,"_x"))
                           ,property=c("entityReference"
                                       ,"xref")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_x")
                                                  ,paste0(pav
                                                          ,"_xx"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_xx")
            
        } else if ("xref" %in% prop_vect) {
            aux_df<-
                data.frame(class=c(paste0(el_id
                                          ,"PLACEHOLDER"))
                           ,id=c(el_id)
                           ,property=c("xref")
                           ,property_attr="rdf:resource"
                           ,property_attr_value=c(paste0(pav
                                                         ,"_xr"))
                           ,property_value="")
            
            el_id<-
                paste0(pav
                       ,"_xr")
        } else {
            #in case, there's no such properties in the property vector,
            #there's no need for auxiliary df
            aux_df<-NULL
        }
        
        #build element df
        dFrame$id<-el_id 
        dFrame$property_attr<-"rdf:datatype"
        dFrame$property_attr_value<-"http://www.w3.org/2001/XMLSchema#string"
        
        #change order
        dFrame<-
            dFrame %>%
            dplyr::select(class
                          ,id
                          ,property
                          ,property_attr
                          ,property_attr_value
                          ,property_value) %>%
            #add that auxiliary dataframe
            rbind.data.frame(aux_df)
        
        return(dFrame)
    }
######################################## internal_string_to_df_inner_inner ########################################
# ######################################## internal_string_to_df_inner_inner ########################################
# internal_string_to_df_inner_inner<-
#     function(string
#              ,el_id=""
#              ,pav=""
#              ,prop_vect){
#         require(stringr)
#         pattern = "([[:alpha:]]*?)=(.*?)\\{class=(.*?)\\}"
#         #search for a given pattern in the string
#         
#         dFrame<-
#             string %>%
#             stringr::str_match_all(pattern) %>%
#             .[[1]] %>%
#             as.data.frame
#         
#         #if resultant dFrame does not have rows, return null
#         if(nrow(dFrame)<1){
#             return(NULL)
#         }
#         
#         #... and take only pertaining columns of the hits
#         #these numbers are hard-coded due to the pattern is known 
#         #and expected to be one and only
#         dFrame<-dFrame[,c(2:4)]
#         
#         #again, pattern is known and that's what it is
#         colnames(dFrame)<-
#             c("property"
#               ,"property_value"
#               ,"class")
#         
#         #exclude all NA values
#         dFrame[dFrame=="NA"]<-NA
#         dFrame<-
#             dFrame %>% 
#             filter(!is.na(property_value))
#         
#         #if resultant dFrame does not have rows, return null
#         if(nrow(dFrame)<1){
#             return(NULL)
#         }
#         
#         #if it's a string with xrefs -- add corresponding 
#         #joining lines (see below) and change ids accordingly
#         #to account for appropriate id nesting
#         if("entityReference" %in% prop_vect){
#             #since the class to which the xref belongs is not known
#             #use a PLACEHOLDER instead
#             aux_df<-
#                 data.frame(class=c(paste0(el_id
#                                           ,"PLACEHOLDER")
#                                    ,paste0(el_id
#                                            ,"PLACEHOLDERReference"))
#                            ,id=c(el_id
#                                  ,paste0(pav
#                                          ,"_x"))
#                            ,property=c("entityReference"
#                                        ,"xref")
#                            ,property_attr="rdf:resource"
#                            ,property_attr_value=c(paste0(pav
#                                                          ,"_x")
#                                                   ,paste0(pav
#                                                           ,"_xx"))
#                            ,property_value="")
#             
#             el_id<-
#                 paste0(pav
#                        ,"_xx")
#             
#         } else if ("xref" %in% prop_vect) {
#             aux_df<-
#                 data.frame(class=c(paste0(el_id
#                                           ,"PLACEHOLDER"))
#                            ,id=c(el_id)
#                            ,property=c("xref")
#                            ,property_attr="rdf:resource"
#                            ,property_attr_value=c(paste0(pav
#                                                          ,"_xr"))
#                            ,property_value="")
#             
#             el_id<-
#                 paste0(pav
#                        ,"_xr")
#         } else {
#             #in case, there's no xref references,
#             #there's no need for auxiliary df
#             aux_df<-NULL
#         }
#         
#         #build element df
#         dFrame$id<-el_id 
#         dFrame$property_attr<-"rdf:datatype"
#         dFrame$property_attr_value<-"http://www.w3.org/2001/XMLSchema#string"
#         
#         #change order
#         dFrame<-
#             dFrame %>%
#             dplyr::select(class
#                           ,id
#                           ,property
#                           ,property_attr
#                           ,property_attr_value
#                           ,property_value) %>%
#             #add that auxiliary dataframe
#             rbind.data.frame(aux_df)
#         
#         return(dFrame)
#     }
# ######################################## internal_string_to_df_inner_inner ########################################