1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
use crate::lowlevel::level0::Superblock;
use crate::lowlevel::level1::{BTreeNode, BTreeNodeChild, LocalHeap, SymbolTableEntry};
use crate::lowlevel::level2::DataObject;
use crate::{Error, ErrorKind, Result};
use std::fs::File;
use std::io::{BufReader, Read, Seek};
use std::path::{Component, Path, PathBuf};

/// HDF5 file.
#[derive(Debug)]
pub struct Hdf5File<T = File> {
    io: T,
    superblock: Superblock,
}
impl Hdf5File<File> {
    /// Makes a new `Hdf5File` instance by opening the specified file.
    pub fn open_file<P: AsRef<Path>>(path: P) -> Result<Self> {
        let file = track!(File::open(path).map_err(Error::from))?;
        track!(Self::open(file))
    }
}
impl<T> Hdf5File<T>
where
    T: Read + Seek,
{
    /// Makes a new `Hdf5File` instance by reading data from the given I/O stream.
    pub fn open(mut io: T) -> Result<Self> {
        let superblock = track!(Superblock::from_reader(&mut io))?;
        Ok(Self { io, superblock })
    }

    /// Returns an iterator that iterates over the paths of all objects stored in the file.
    pub fn object_paths<'a>(&'a mut self) -> Result<impl 'a + Iterator<Item = Result<PathBuf>>> {
        let mut io = BufReader::new(&mut self.io);
        let root = track!(Node::new(
            &mut io,
            &self.superblock.root_group_symbol_table_entry,
        ))?;
        Ok(Objects::new(io, root))
    }

    /// Returns a data object associated with the given path.
    pub fn get_object<P: AsRef<Path>>(&mut self, path: P) -> Result<Option<DataObject>> {
        let mut io = BufReader::new(&mut self.io);
        let mut node = track!(Node::new(
            &mut io,
            &self.superblock.root_group_symbol_table_entry,
        ))?;

        let mut components = path.as_ref().components().peekable();
        track_assert_eq!(
            components.next(),
            Some(Component::RootDir),
            ErrorKind::InvalidInput
        );

        while let Some(component) = components.next() {
            if let Component::Normal(name) = component {
                let name = track_assert_some!(name.to_str(), ErrorKind::InvalidInput);
                if components.peek().is_some() {
                    if let Some(child) = track!(node.get_dir(&mut io, name))? {
                        node = child;
                    } else {
                        return Ok(None);
                    }
                } else if let Some(data) = track!(node.get_data(&mut io, name))? {
                    return Ok(Some(data));
                } else {
                    return Ok(None);
                }
            } else {
                track_panic!(ErrorKind::InvalidInput);
            }
        }
        track_panic!(ErrorKind::InvalidInput);
    }
}

#[derive(Debug)]
pub struct Node {
    dir: PathBuf,
    b_tree_node: BTreeNode,
    local_heap: LocalHeap,
}
impl Node {
    pub fn new<T>(mut io: T, symbol_table: &SymbolTableEntry) -> Result<Self>
    where
        T: Read + Seek,
    {
        let b_tree_node = track!(symbol_table.b_tree_node(&mut io))?;
        let b_tree_node = track_assert_some!(b_tree_node, ErrorKind::InvalidInput);

        let local_heap = track!(symbol_table.local_heap(&mut io))?;
        let local_heap = track_assert_some!(local_heap, ErrorKind::InvalidInput);
        Ok(Self {
            dir: PathBuf::from("/"),
            b_tree_node,
            local_heap,
        })
    }

    pub fn try_new<T>(mut io: T, symbol_table: &SymbolTableEntry) -> Result<Option<Self>>
    where
        T: Read + Seek,
    {
        let b_tree_node = track!(symbol_table.b_tree_node(&mut io))?;
        let b_tree_node = if let Some(b_tree_node) = b_tree_node {
            b_tree_node
        } else {
            return Ok(None);
        };

        let local_heap = track!(symbol_table.local_heap(&mut io))?;
        let local_heap = track_assert_some!(local_heap, ErrorKind::InvalidInput);
        Ok(Some(Self {
            dir: PathBuf::from("/"),
            b_tree_node,
            local_heap,
        }))
    }

    fn get_btree_node_child<T>(&self, mut io: T, name: &str) -> Result<Option<BTreeNodeChild>>
    where
        T: Read + Seek,
    {
        let mut found = false;
        let mut index = 0;
        for key in self
            .b_tree_node
            .keys(self.local_heap.clone(), &mut io)
            .skip(1)
        {
            let key = track!(key)?;

            if name <= key.as_str() {
                found = true;
                break;
            }
            index += 1;
        }
        if !found {
            Ok(None)
        } else {
            let child = track_assert_some!(self.children(&mut io).nth(index), ErrorKind::Other);
            Ok(Some(track!(child)?))
        }
    }

    pub fn get_dir<T>(&self, mut io: T, name: &str) -> Result<Option<Self>>
    where
        T: Read + Seek,
    {
        let child = track!(self.get_btree_node_child(&mut io, name))?;
        match child {
            None => Ok(None),
            Some(BTreeNodeChild::Intermediate(child)) => {
                let child = Self {
                    dir: self.dir.clone(),
                    b_tree_node: child,
                    local_heap: self.local_heap.clone(),
                };
                track!(child.get_dir(io, name))
            }
            Some(BTreeNodeChild::GroupLeaf(child)) => {
                for entry in &child.entries {
                    let child_name = track!(entry.link_name(&mut io, Some(&self.local_heap)))?;
                    let child_name = track_assert_some!(child_name, ErrorKind::InvalidFile);
                    if child_name == name {
                        let mut child = track!(Node::new(&mut io, &entry))?;
                        child.dir = self.dir.clone();
                        child.dir.push(name);
                        return Ok(Some(child));
                    }
                }
                Ok(None)
            }
        }
    }

    pub fn get_data<T>(&self, mut io: T, name: &str) -> Result<Option<DataObject>>
    where
        T: Read + Seek,
    {
        let child = track!(self.get_btree_node_child(&mut io, name))?;
        match child {
            None => Ok(None),
            Some(BTreeNodeChild::Intermediate(child)) => {
                let child = Self {
                    dir: self.dir.clone(),
                    b_tree_node: child,
                    local_heap: self.local_heap.clone(),
                };
                track!(child.get_data(io, name))
            }
            Some(BTreeNodeChild::GroupLeaf(child)) => {
                for entry in &child.entries {
                    let child_name = track!(entry.link_name(&mut io, Some(&self.local_heap)))?;
                    let child_name = track_assert_some!(child_name, ErrorKind::InvalidFile);
                    if child_name == name {
                        let data = track!(entry.get_data_object(&mut io))?;
                        return Ok(Some(data));
                    }
                }
                Ok(None)
            }
        }
    }

    pub fn children<'a, T>(&'a self, io: T) -> impl 'a + Iterator<Item = Result<BTreeNodeChild>>
    where
        T: 'a + Read + Seek,
    {
        self.b_tree_node.children(io)
    }
}

#[derive(Debug)]
struct Objects<T> {
    io: T,
    nodes: Vec<Node>,
    paths: Vec<PathBuf>,
}
impl<T> Objects<T>
where
    T: Read + Seek,
{
    fn new(io: T, root: Node) -> Self {
        Self {
            io,
            nodes: vec![root],
            paths: Vec::new(),
        }
    }

    fn next_object_path(&mut self) -> Result<Option<PathBuf>> {
        if let Some(path) = self.paths.pop() {
            return Ok(Some(path));
        }

        while let Some(node) = self.nodes.pop() {
            for child in node.children(&mut self.io).collect::<Vec<_>>() {
                let child = track!(child)?;
                match child {
                    BTreeNodeChild::Intermediate(child) => {
                        let child = Node {
                            dir: node.dir.clone(),
                            b_tree_node: child,
                            local_heap: node.local_heap.clone(),
                        };
                        self.nodes.push(child);
                    }
                    BTreeNodeChild::GroupLeaf(child) => {
                        for entry in &child.entries {
                            let name =
                                track!(entry.link_name(&mut self.io, Some(&node.local_heap)))?;
                            let name = track_assert_some!(name, ErrorKind::InvalidFile);

                            let mut path = node.dir.clone();
                            path.push(name);
                            self.paths.push(path.clone());

                            if let Some(mut grand_child) =
                                track!(Node::try_new(&mut self.io, &entry))?
                            {
                                grand_child.dir = path;
                                self.nodes.push(grand_child);
                            }
                        }
                    }
                }
            }
            if !self.paths.is_empty() {
                break;
            }
        }

        Ok(self.paths.pop())
    }
}
impl<T> Iterator for Objects<T>
where
    T: Read + Seek,
{
    type Item = Result<PathBuf>;

    fn next(&mut self) -> Option<Self::Item> {
        track!(self.next_object_path()).transpose()
    }
}