# create the group paths removing the datetime at the end using the delimiter "/"
# it should not remove folders with less than 3 digits. See regex {4}
# because 4 digits could mean the year

# Regex: http://stackoverflow.com/a/6508020/5270873

# form the paths of only the groups
hFile <- file.path("./", "WOODLIB.03.hdf5")
df <- h5ls(hFile, recursive = 3)


df2 <- df %>%
    filter(otype == "H5I_GROUP") %>%
    select(-c(dclass, dim)) %>%
    mutate(paths = ifelse(nchar(group) == 1,  
                          paste0(group, name), 
                          paste(group, name, sep = "/"))) %>%
    mutate(casePaths = gsub("(.*)/[0-9]{4}.*","\\1", paths)) %>%
    select(-c(otype, name)) %>%
    distinct(casePaths, .keep_all = TRUE)

df2
source("Rutils.R")

# new function working with grepl and %in%
hGroup.exists <- function(hFile, hGroup) {
    hGroup <- ifelse(!grepl("^/", hGroup), paste0("/", hGroup), hGroup)
    groups <- get.group.paths(hFile)

    if (hGroup %in% groups)
        return(TRUE)
    else
        return(FALSE)
}    


hGroup.exists("WOODLIB.03.hdf5", "11")
hGroup.exists("WOODLIB.03.hdf5", "BROWN")

hGroup.exists("WOODLIB.01.hdf5", "ExampleGuo")
hGroup.exists("WOODLIB.01.hdf5", "/11")
hGroup.exists("WOODLIB.011.hdf5", "HAGBR")
hGroup.exists("WOODLIB.011.hdf5", "BROWN")

hGroup.exists("WOODLIB.03.hdf5", "1/2")
hGroup.exists("WOODLIB.03.hdf5", "/1/22")
hGroup.exists("WOODLIB.03.hdf5", "11/12")

# [1] TRUE
# [1] FALSE
# [1] TRUE
# [1] TRUE
# [1] TRUE
# [1] FALSE
# [1] TRUE
# [1] TRUE
# [1] FALSE
# get.group.paths <- function(hFile) {
# 
#     hFile <- file.path(wells.dir, hFile)
#     df <- h5ls(hFile, recursive = 3)
# 
#     df2 <- df %>%
#         filter(otype == "H5I_GROUP") %>%
#         select(-c(dclass, dim)) %>%
#         mutate(paths = ifelse(nchar(group) == 1,  
#                               paste0(group, name), 
#                               paste(group, name, sep = "/"))) %>%
#         mutate(casePaths = gsub("(.*)/[0-9]{4}.*","\\1", paths)) %>%
#         select(-c(otype, name)) %>%
#         distinct(casePaths, .keep_all = TRUE)
#     return(df2$casePaths)
# } 



# call the function above
get.group.paths("WOODLIB.03.hdf5") 
cat("\n")
get.group.paths("WOODLIB.01.hdf5")
cat("\n")
get.group.paths("WOODLIB.011.hdf5")
# testing if hGroup.exists works. 
# this chunk will create a field/well if they do not exist

source("Rutils.R")

hFile <- "WOODLIB.01.hdf5"
wells.dir <- "./"
group.paths <- get.group.paths(hFile)  
group.paths

fieldName <- "111" 
wellName <- "Example_04"
.fieldName <- paste0("/", fieldName)
field.well <- paste(.fieldName, wellName, sep = "/")
# field.well


if (!field.well %in% group.paths) {
    cat("\nGroup: ", field.well, " DOES NOT exist \n")
    if (!hGroup.exists(hFile, fieldName)) {
        h5createGroup(hFile, fieldName)
        cat("Group: ", fieldName, "just created\n")
    } else {
       cat("\t but group ", fieldName, " already exists\n")
    }
    h5createGroup(hFile, field.well)
    cat("\t", wellName, "well just added")
} else  {
    cat("\n Group", field.well," already exists")
}

H5close()
# 
# field.well %in% group.paths
# hGroup.exists(hFile, fieldName)

new function to save to HDF5

source("VLP.R")

#' Save the well parameters in an HDF5 file
#' 
save.well.data <- function() {

    # well.data <- as.data.frame(well.params())
    params <- well.params()         # get the core well parameters
    well.data <- params$out.data    # get only the input data
    well.calc <- params$out.calc    # get the core calculations. no iterations here

    well.name <- well.data$well.name  # extract the well name

    # build the full filename
    wells.dir <- "./"
    wellFile <- file.path(wells.dir, "WOODLIB.01.hdf5")

    # add FIELD group and WELL group
    field <- "HAGBR"            # field name

    # add a well record
    hg <- add.wellRecord(wellFile, field, well.name)

    ds.well.data <- paste(hg, "well.data", sep = "/")
    ds.well.calc <- paste(hg, "well.calc", sep = "/")

    h5write(well.data, wellFile, ds.well.data)
    h5write(well.calc, wellFile, ds.well.calc)
    H5close()
    return(hg)
}   

save.well.data()

Code that works

source("VLP.R")

# get well parameters: input and calculated
params <- well.params()

# extract only the list with data
well.data <- params$out.data
well.calc <- params$out.calc

# get the well name from the parameters
well.name <- well.data$well.name

# wellFile <- paste(paste("./data", well.name, sep = "/"), "hdf5", sep = ".")
# save(well.data, file = well.file)

# build the full filename
# wells.dir <- "./"
# wellFile <- file.path(wells.dir, "WOODLIB.001.hdf5")
wellFile <- model.parameters$wellFile


# add FIELD group and WELL group
field <- "HAGBR"            # field name

# add a well record
hg <- add.wellRecord(wellFile, field, well.name)
cat("\n", hg)

# add well data
ds.well.data <- paste(hg, "well.data", sep = "/")
ds.well.calc <- paste(hg, "well.calc", sep = "/")

# write well data to HDF5
h5write(well.data, wellFile, ds.well.data)
h5write(well.calc, wellFile, ds.well.calc)
H5close()
source("Rutils.R")

fieldName <- "HAGBR"    
wellName <- "Example01"

# build the full filename
wells.dir <- "./"
hFile <- file.path(wells.dir, "WOODLIB.03.hdf5")

if (!file.exists(hFile)) 
    fid <- H5Fcreate(hFile) #else fid <- H5Fopen(hFile)

hGroup.exists(hFile, fieldName)
hGroup.exists(hFile, wellName)
wellName <- "Example01"
hFile <- file.path(wells.dir, "WOODLIB.03.hdf5")
h5createGroup(hFile, wellName)
hFile <- file.path(wells.dir, "WOODLIB.03.hdf5")
df <- h5ls(hFile, recursive = 3)

if (!field.well %in% unique(df$group)) {
    cat(field.well, " not in df.group\n")
    if (!field %in% unique(df$group)) {
        cat("\t", field, " not in df.group\n")
    } else {
        cat(field, " field exists")
        # H5I_GROUP
        if (!well %in% unique(df$name)) 
    }
}
H5close()
file = H5Fopen (hFile, flags = h5default("H5F_ACC_RD"))
status = H5Gget_info (file)
# form the paths of only the groups
hFile <- file.path(wells.dir, "WOODLIB.011.hdf5")
df <- h5ls(hFile, recursive = 3)

df2 <- df %>%
    filter(otype == "H5I_GROUP") %>%
    select(-c(dclass, dim)) %>%
    mutate(paths = ifelse(nchar(group) == 1,  
                          paste0(group, name), 
                          paste(group, name, sep = "/")))
df2
# show how many characters the group column has
df2 <- df %>%
    filter(otype == "H5I_GROUP") %>%
    mutate(paths = ifelse(nchar(group) == 1, 1, nchar(group)))
df2
# Regex: http://stackoverflow.com/a/6508020/5270873

# form the paths of only the groups
hFile <- file.path(wells.dir, "WOODLIB.011.hdf5")
df <- h5ls(hFile, recursive = 3)


df2 <- df %>%
    filter(otype == "H5I_GROUP") %>%
    select(-c(dclass, dim)) %>%
    mutate(paths = ifelse(nchar(group) == 1,  
                          paste0(group, name), 
                          paste(group, name, sep = "/"))) %>%
    mutate(casePaths = gsub("(.*)/[0-9][0-9][0-9].*","\\1", paths)) %>%
    select(-c(otype, name)) %>%
    distinct(casePaths, .keep_all = TRUE)
df2

regex

rs<-c("copyright @ The Society of mo located @ my house","I want you to meet me @ the coffeshop")
s<-gsub("(.*)@.*","\\1", rs)
s
rs <- "/HAGBR/ExampleGuo/20170403.122239"
s <- gsub("(.*)/[0-9].*","\\1", rs)
s
# will work only if there are numbers to the right of the slash
rs <- "/HAGBR/ExampleGuo"
s <- gsub("(.*)/[0-9].*","\\1", rs)
s
# But what about a folder `222` which is not a datetime?
# will work only if there are numbers to the right of the slash
rs <- "/HAGBR/ExampleGuo/222"
s <- gsub("(.*)/[0-9].*","\\1", rs)
s
# this won't work
# [1] "/HAGBR/ExampleGuo"
# if we add {4} after [0-9], the group `222` will be allowed
# a folder `222` which is not a datetime
# will work only if there are numbers to the right of the slash
rs <- "/HAGBR/ExampleGuo/222"
s <- gsub("(.*)/[0-9]{4}.*","\\1", rs)
s
# [1] "/HAGBR/ExampleGuo/222"
# if we have the year as the end group, it will be removed
# if we add {4} after [0-9], the group `222` will be allowed
# a folder `222` which is not a datetime
# will work only if there are numbers to the right of the slash
rs <- "/HAGBR/ExampleGuo/2017"
s <- gsub("(.*)/[0-9]{4}.*","\\1", rs)
s
# [1] "/HAGBR/ExampleGuo"
# what we are looking for


f0nzie/rNodal documentation built on Oct. 30, 2017, 4:03 a.m.