Change download URL & store metadata for Xena

Changed `base_url` for downloading data from the Xena browser from
https://genome-cancer.ucsc.edu/download/public/xena/TCGA/TCGA.PANCAN.sampleMap/
to https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/. This new location
seems to have resolved the unstandardized mutation effects reported in
cognoma#2.

Added json metadata files to `download` providing version info at time of
download. Thanks @jingchunzhu for the suggestion. See
https://groups.google.com/forum/#!msg/ucsc-cancer-genomics-browser/eg6nJOFSefw/wO0wNrMeAgAJ

1.TCGA-download.ipynb

@@ -64,7 +64,7 @@
    },
    "outputs": [],
    "source": [
-    "base_url = 'https://genome-cancer.ucsc.edu/download/public/xena/TCGA/TCGA.PANCAN.sampleMap/'\n",
+    "base_url = 'https://tcga.xenahubs.net/download/TCGA.PANCAN.sampleMap/'\n",
     "\n",
     "names = [\n",
     "    'PANCAN_clinicalMatrix',\n",
@@ -81,6 +81,22 @@
    },
    "outputs": [],
    "source": [
+    "# Download metadata\n",
+    "for name in names:\n",
+    "    url = base_url + name + '.json'\n",
+    "    path = os.path.join('download', name + '.json')\n",
+    "    urlretrieve(url, path)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "# Download data\n",
     "for name in names:\n",
     "    url = base_url + name\n",
     "    path = os.path.join('download', name + '.tsv')\n",