Fix reading HDF5 from buffer

alubbock · Nov 3, 2018 · 6648cfb · 6648cfb
1 parent f34ed22
commit 6648cfb
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/doc/conf.py b/doc/conf.py
@@ -18,7 +18,7 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../'))
 
 # -- General configuration ------------------------------------------------
 

diff --git a/doc/tutorial.ipynb b/doc/tutorial.ipynb
@@ -61,14 +61,26 @@
     "First, specify a file to load. This can be done as a string filename, but here we load an example dataset from the thunor package itself, but you can also another filename."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# If \"import thunor\" fails, you may need to uncomment the following two lines\n",
+    "# import os, sys\n",
+    "# sys.path.insert(0, os.path.abspath('../'))\n",
+    "import thunor"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import pkg_resources\n",
-    "hts007_file = pkg_resources.resource_filename('thunor', 'testdata/hts007.h5')"
+    "hts007_file = pkg_resources.resource_stream('thunor', 'testdata/hts007.h5')"
    ]
   },
   {

diff --git a/thunor/io.py b/thunor/io.py
@@ -930,7 +930,7 @@ def _read_hdf_unstacked(filename_or_buffer):
             'path': 'data.h5',
             'driver': 'H5FD_CORE',
             'driver_core_backing_store': 0,
-            'driver_core_image': filename_or_buffer
+            'driver_core_image': filename_or_buffer.read()
         })
     with pd.HDFStore(**hdf_kwargs) as hdf:
         df_assays = hdf['assays']