Fixed multiple dispatch issues on io.jl

Related to issue #74, io.jl is no more modifying functionality of LightXML
2026-09-26 03:44:45 +00:00 · 2017-01-21 10:30:23 +02:00
parent c1b5d2f7ed
commit 9b4c1a4c5e
5 changed files with 215 additions and 313 deletions
@@ -30,7 +30,7 @@ module Testing
 end

 include("io.jl")
-export Xdmf, h5file, xmffile, has_child, get_child, new_dataitem
+export Xdmf, h5file, xmffile, xdmf_filter, new_dataitem, get_temporal_collection

 include("fields.jl")
 export Field, DCTI, DVTI, DCTV, DVTV, CCTI, CVTI, CCTV, CVTV, Increment
@@ -3,100 +3,6 @@

 using HDF5
 using LightXML
-importall LightXML
-importall Base
-
-function new_element(name::String, attrs::Dict)
-    x = new_element(name)
-    for (k, v) in attrs
-        x[k] = v
-    end
-    return x
-end
-
-function setindex!(x::XMLElement, content::Any, attr_name::String)
-    set_attribute(x, attr_name, content)
-end
-
-function haskey(x::XMLElement, key::String)
-    return has_child(x, key) || has_attribute(x, key)
-end
-
-function has_child(x::XMLElement, child_name::String)
-    return get_child(x, child_name) != nothing
-end
-
-function get_attribute(x::XMLElement, attr_name::String)
-    attr = attribute(x, attr_name)
-    numeric = tryparse(Int64, attr)
-    isnull(numeric) && (numeric = tryparse(Float64, attr))
-    isnull(numeric) && return attr
-    return get(numeric)
-end
-
-function new_child(xparent::XMLElement, name::String, attrs::Dict)
-    x = new_child(xparent, name)
-    for (k, v) in attrs
-        x[k] = v
-    end
-    return x
-end
-
-""" Basic traverse support, so that it's possible to find data from xml using
-path syntax e.g. /foo/bar[2]/baz[@Name=Frame 1]/DataItem. If several elements
-with same name exists in tree, pick first by default and next ones can be picked
-using [] syntax or [@attr=value] syntax, see [1] for details. For last item use
-[end].
-
-[1] http://www.xdmf.org/index.php/XDMF_Model_and_Format
-"""
-function get_child(x::XMLElement, child_name::String)
-    '/' in child_name && return nothing
-    m = match(r"(\w+)\[(.+)\]", child_name)
-    if m != nothing
-        child_name = m[1]
-    end
-    childs = []
-    for child in child_elements(x)
-        if name(child) == child_name
-            push!(childs, child)
-        end
-    end
-    length(childs) == 0 && return nothing
-    m == nothing && return first(childs)
-    j = tryparse(Int, m[2])
-    isnull(j) || return childs[get(j)]
-    m[2] == "end" && return childs[end]
-    m2 = match(r"@(.+)=(.+)", m[2])
-    m2 == nothing && throw("Unable to parse: $(m[2])")
-    attr_name = convert(String, m2[1])
-    attr_value = convert(String, m2[2])
-    for child in childs
-        has_attribute(child, attr_name) || continue
-        if get_attribute(child, attr_name) == attr_value
-            return child
-        end
-    end
-    throw("Unable to parse: $(m[2])")
-end
-
-function getindex(x::XMLElement, attr_name::String)
-    attr_name = strip(attr_name, '/')
-    child = get_child(x, attr_name)
-    child == nothing || return child
-    has_attribute(x, attr_name) && return get_attribute(x, attr_name)
-    if '/' in attr_name
-        items = map(String, split(attr_name, '/'))
-        attr_name = first(items)
-        length(items) > 1 || throw(KeyError(attr_name))
-        haskey(x, attr_name) || throw(KeyError(attr_name))
-        path = join(items[2:end], '/')
-        new_item = getindex(x, attr_name)
-        return new_item[path]
-    else
-        throw(KeyError(attr_name))
-    end
-end

 type Xdmf
    name :: String
@@ -104,24 +10,6 @@ type Xdmf
    hdf :: HDF5File
 end

-function new_child(xdmf::Xdmf, args...; kwargs...)
-    new_child(xdmf.xml, args...; kwargs...)
-end
-
-function read(xdmf::Xdmf, path::String)
-    result = getindex(xdmf.xml, path)
-    if endswith(path, "DataItem")
-        format = get_attribute(result, "Format")
-        @assert format == "HDF"
-        h5file, path = map(String, split(content(result), ':'))
-        h5file = dirname(xdmf.name) * "/" * h5file
-        isfile(h5file) || throw("Xdmf: h5 file $h5file not found!")
-        return read(xdmf.hdf, path)
-    else
-        return result
-    end
-end
-
 function Xdmf()
    return Xdmf(tempname())
 end
@@ -134,6 +22,7 @@ function xmffile(xdmf::Xdmf)
    return xdmf.name*".xmf"
 end

+""" Initialize a new Xdmf object. """
 function Xdmf(name::String; overwrite=false)
    xdmf = new_element("Xdmf")
    h5file = "$name.h5"
@@ -164,6 +53,175 @@ function Xdmf(name::String; overwrite=false)
    return Xdmf(name, xdmf, hdf)
 end

+""" Return the basic structure of Xdmf document. Creates a new TemporalCollection if not found.
+
+Basic structure for XML part of Xdmf file is
+
+<?xml version="1.0" encoding="utf-8"?>
+<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.1">
+  <Domain>
+    <Grid CollectionType="Temporal" GridType="Collection">
+    </Grid>
+  </Domain>
+</Xdmf>
+
+"""
+function get_temporal_collection(xdmf::Xdmf)
+    domain = find_element(xdmf.xml, "Domain")
+    grid = nothing
+    if domain == nothing
+        debug("Xdmf: creating new temporal collection")
+        domain = new_child(xdmf.xml, "Domain")
+        grid = new_child(domain, "Grid")
+        set_attribute(grid, "CollectionType", "Temporal")
+        set_attribute(grid, "GridType", "Collection")
+    end
+    grid = find_element(domain, "Grid")
+    return grid
+end
+
+""" Returns some spesific child xml element from a array of XMLElement based on,
+"Xdmf extensions" see [1] for details.
+
+Parameters
+----------
+child_elements :: Vector{XMLElement}
+    A vector of XMLElements where to perform filtering.
+child_name :: String
+    Child element name, maybe containing Xdmf instructions
+
+Returns
+-------
+nothing if nothing is found, otherwise XMLElement matching to filtering
+
+Examples
+--------
+julia> grid1 = new_element("Grid")
+julia> add_text(grid1, "I am first grid")
+julia> grid2 = new_element("Grid")
+julia> add_text(grid2, "I am second grid")
+julia> set_attribute(grid2, "Name", "Frame 2")
+julia> grid3 = new_element("Grid")
+julia> add_text(grid3, "I am third grid")
+julia> grids = [grid1, grid2, grid3]
+
+To return second Grid element, one can use
+
+julia> xdmf_filter(grids, "Grid[2]")
+
+To return Grid which has attribute Name="Frame 2", use
+
+julia> xdmf_filter(grids, "Grid[@name=Frame 2]")
+
+To pick last Grid, use [end], e.g.
+
+julia> xdmf_filter(grids, "Grid[end]").
+
+References
+----------
+[1] http://www.xdmf.org/index.php/XDMF_Model_and_Format
+"""
+function xdmf_filter(child_elements, child_name)
+    if '/' in child_name # needs path traversal
+        return nothing
+    end
+
+    # filter children elements using syntax child[X] -> rename child_name
+    m = match(r"(\w+)\[(.+)\]", child_name)
+    if m != nothing
+        child_name = m[1]
+    end
+
+    # first find any relevant child elements (has same tag)
+    childs = []
+    for child in child_elements
+        if LightXML.name(child) == child_name
+            push!(childs, child)
+        end
+    end
+
+    # childs not found at all
+    length(childs) == 0 && return nothing
+
+    # by default return first
+    m == nothing && return first(childs)
+
+    # if [end] return last
+    m[2] == "end" && return childs[end]
+
+    # otherwise try parse int and return nth children from list
+    parsed_int = tryparse(Int, m[2])
+    if !isnull(parsed_int)
+        idx = get(parsed_int)
+        if (idx > 0) && (idx <= length(childs))
+            return childs[idx]
+        else
+            # wrong index
+            return nothing
+        end
+    end
+
+    # [X] is something else than integer,  filter children elements using syntax child[@attr=value]
+    m2 = match(r"@(.+)=(.+)", m[2])
+    m2 == nothing && throw("Unable to parse: $(m[2])")
+    attr_name = convert(String, m2[1])
+    attr_value = convert(String, m2[2])
+    for child in childs
+        has_attribute(child, attr_name) || continue
+        if attribute(child, attr_name) == attr_value
+            return child
+        end
+    end
+
+    # nothing found
+    return nothing
+end
+
+""" Traverse XML path. Xdmf filtering can be used, so it's possible to find
+data from xml using syntax e.g. 
+
+julia> traverse(xdmf, x, "/Domain/Grid[2]/Grid[@Name=Frame 1]/DataItem")
+"""
+function traverse(xdmf::Xdmf, x::XMLElement, attr_name::String)
+    attr_name = strip(attr_name, '/')
+
+    if has_attribute(x, attr_name)
+        return attribute(x, attr_name)
+    end
+
+    childs = child_elements(x)
+
+    if '/' in attr_name
+        items = split(attr_name, '/')
+        new_item = xdmf_filter(childs, first(items))
+        new_path = join(items[2:end], '/')
+        return traverse(xdmf, new_item, new_path)
+    end
+    
+    child = xdmf_filter(childs, attr_name)
+    return child
+end
+
+""" Read data from Xdmf file.
+
+Traversing is supported, so one can easily traverse XML tree e.g.
+julia> read(xdmf, "/Domain/Grid/Grid[2]/Geometry")
+"""
+function read(xdmf::Xdmf, path::String)
+    result = traverse(xdmf, xdmf.xml, path)
+    if endswith(path, "DataItem")
+        format = attribute(result, "Format"; required=true)
+        @assert format == "HDF"
+        h5file, path = map(String, split(content(result), ':'))
+        h5file = dirname(xdmf.name) * "/" * h5file
+        isfile(h5file) || throw("Xdmf: h5 file $h5file not found!")
+        return read(xdmf.hdf, path)
+    else
+        return result
+    end
+end
+
+
 function save!(xdmf::Xdmf)
    doc = XMLDocument()
    set_root(doc, xdmf.xml)
@@ -488,20 +488,6 @@ function (solver::Solver)(field_name::AbstractString, time::Float64)
    return merge(fields...)
 end

-function get_temporal_collection(xdmf::Xdmf)
-    domain = find_element(xdmf.xml, "Domain")
-    grid = nothing
-    if domain == nothing
-        info("Xdmf: creating new temporal collection")
-        domain = new_child(xdmf.xml, "Domain")
-        grid = new_child(domain, "Grid")
-        set_attribute(grid, "CollectionType", "Temporal")
-        set_attribute(grid, "GridType", "Collection")
-    end
-    grid = find_element(domain, "Grid")
-    return grid
-end
-
 """ Default update for solver. """
 function update!{S}(solver::Solver{S}; show_info=true)
    u = solver.u
@@ -540,7 +526,8 @@ function update_xdmf!{S}(solver::Solver{S}; show_info=true)
    geom_type = (ndim == 2 ? "XY" : "XYZ")
    data_node_ids = new_dataitem(xdmf, "/Node IDs", node_ids)
    data_geometry = new_dataitem(xdmf, "/Geometry", X)
-    geometry = new_element("Geometry", Dict("Type" => geom_type))
+    geometry = new_element("Geometry")
+    set_attribute(geometry, "Type", geom_type)
    add_child(geometry, data_geometry)

    # 2. save topology
@@ -588,7 +575,8 @@ function update_xdmf!{S}(solver::Solver{S}; show_info=true)

    # 3. save solved field
    frame = new_element("Grid")
-    new_child(frame, "Time", Dict("Value" => solver.time))
+    time = new_child(frame, "Time")
+    set_attribute(time, "Value", solver.time)
    add_child(frame, geometry)
    for topo in topology
        add_child(frame, topo)
@@ -420,10 +420,12 @@ function update_xdmf!(solver::Solver{Modal}; show_info=true)
        info("Creating frequency frame f=$(round(freq, 3)), path=$path")

        frame = new_element("Grid")
-        new_child(frame, "Time", Dict("Value" => freq))
+        time = new_child(frame, "Time")
+        set_attribute(time, "Value", freq)

        # add geometry
-        geometry = new_element("Geometry", Dict("Type" => geom_type))
+        geometry = new_element("Geometry")
+        set_attribute(geometry, "Type", geom_type)
        data_node_ids = new_dataitem(xdmf, "/Node IDs", node_ids)
        data_geometry = new_dataitem(xdmf, "/Geometry", X)
        add_child(geometry, data_geometry)