HDF5 virtual dataset access issue

VDS issue.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import h5py\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'2.9.0'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
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   "source": [
    "h5py.__version__"
   ]
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  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
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    {
     "data": {
      "text/plain": [
       "'1.10.4'"
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     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "h5py.version.hdf5_version"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Make two source files with regular datasets, and make the second one read-only:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "with h5py.File('src1.h5', 'w') as f:\n",
    "    f['data'] = np.arange(0, 10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "!rm -rf src2.h5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "with h5py.File('src2.h5', 'w') as f:\n",
    "    f['data'] = np.arange(10, 20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "!chmod -w src2.h5"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Assemble a virtual dataset in a third file:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "layout = h5py.VirtualLayout((2, 10), dtype=np.int64)\n",
    "vsrc1 = h5py.VirtualSource(\"src1.h5\",  \"data\", (10,), dtype=np.int64)\n",
    "vsrc2 = h5py.VirtualSource(\"src2.h5\",  \"data\", (10,), dtype=np.int64)\n",
    "layout[0] = vsrc1\n",
    "layout[1] = vsrc2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "with h5py.File('virt.h5', 'w') as f:\n",
    "    f.create_virtual_dataset('data', layout)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If we open the third file read-only, we can see all its data:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9],\n",
       "       [10, 11, 12, 13, 14, 15, 16, 17, 18, 19]])"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with h5py.File('virt.h5', 'r') as f:\n",
    "    arr = f['data'][:]\n",
    "arr"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "But if we open it for read+write, the data from `src2.h5` (read-only) is not accessible."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0, 1, 2, 3, 4, 5, 6, 7, 8, 9],\n",
       "       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "with h5py.File('virt.h5', 'r+') as f:\n",
    "    arr = f['data'][:]\n",
    "arr"
   ]
  }
 ],
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