New notebooks - Bundles, FHIR exploration, etc.

Updates for KF production FHIR FHIR and DRS examples Updates for NCBI DRS Custom dbGaP frequency distributions Starter KIt client examples Seven Bridges DRS import exploration Seven Bridges DRS download costs NCBI DRS Bundle exploration Imaging Data Commons DICOM DRS access - viewer example
ga4gh · Oct 17, 2022 · 88d014a · 88d014a
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diff --git a/.gitignore b/.gitignore
@@ -142,3 +142,4 @@ dmypy.json
 
 # Mac OS X
 .DS_Store
+*.dcm
diff --git a/notebooks/Ewings Sarcoma - FHIR and DRS.ipynb b/notebooks/Ewings Sarcoma - FHIR and DRS.ipynb
diff --git a/notebooks/FASPNotebook14-SRAExample.ipynb b/notebooks/FASPNotebook14-SRAExample.ipynb
@@ -6,8 +6,8 @@
    "source": [
     "<img src=\"../fasp/runner/credits/images/FASPNotebook10.jpg\" style=\"float: right;\">\n",
     "\n",
-    "## Obtain Thousand Genomes files from SRA DRS and submit to Seven Bridges WES\n",
-    "This notebook explores use of the SRA DRS server. It is derived from FASPScript14.py but has been adapted to use a Seven Bridges WES service. \n",
+    "## Obtain Thousand Genomes files from NCBI DRS and submit to Seven Bridges WES\n",
+    "This notebook explores use of the NCBI DRS server. It is derived from FASPScript14.py but has been adapted to use a Seven Bridges WES service. \n",
     "\n",
     "The mapping of DRS ids to SRA accessions may be done in different ways and the process to do so is in flux.\n",
     "\n",
@@ -16,20 +16,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "_Retrieving the query_\n",
+      "Retrieving the query\n",
       "____Page1_______________\n",
       "____Page2_______________\n",
       "____Page3_______________\n",
       "____Page4_______________\n",
       "____Page5_______________\n",
-      "____Page6_______________\n"
+      "____Page6_______________\n",
+      "____Page7_______________\n"
      ]
     },
     {
@@ -88,7 +89,7 @@
        "2     NA18943  9f38253b281c7e9c99e4bdbececd8e2f  SRR1606910"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 1,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -119,20 +120,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "_Retrieving the query_\n",
+      "Retrieving the query\n",
       "____Page1_______________\n",
       "____Page2_______________\n",
       "____Page3_______________\n",
       "____Page4_______________\n",
       "____Page5_______________\n",
-      "____Page6_______________\n"
+      "____Page6_______________\n",
+      "____Page7_______________\n"
      ]
     },
     {
@@ -143,7 +145,7 @@
        " ['NA18943', '9f38253b281c7e9c99e4bdbececd8e2f', 'SRR1606910']]"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 2,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -162,7 +164,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -175,23 +177,24 @@
     {
      "data": {
       "text/plain": [
-       "{'access_methods': [{'access_id': 'b5f46aadbcb48d7141104db0440feb63cd4e61c8',\n",
-       "   'region': 's3.us-east-1',\n",
-       "   'type': 'https'},\n",
-       "  {'access_id': '1bc0bc010f0edf4ef18af594acdba5db864db67e',\n",
+       "{'access_methods': [{'access_id': '1e4846c05c81a49f684e7f940ffbd3a98e5f0e335f019ee4d32d85c72096b743',\n",
        "   'region': 'gs.US',\n",
        "   'type': 'https'},\n",
-       "  {'access_id': '722d3466edf7ad5f6797f9774e21b368c45ad5b1', 'type': 'https'}],\n",
+       "  {'access_id': 'b14572d74b5aafe87a0fcc873050d6c3993f27338cdd088b5883aed4b118f0c8',\n",
+       "   'type': 'https'},\n",
+       "  {'access_id': '0623f9350999297e5fa3a77a05c08b8cf1fbd10ef4e392c0d52dde9a4e469a85',\n",
+       "   'region': 's3.us-east-1',\n",
+       "   'type': 'https'}],\n",
        " 'checksums': [{'checksum': 'fb1cfb04d3ef99d07c21f9dbf87ccc68',\n",
        "   'type': 'md5'}],\n",
        " 'created_time': '2013-02-25T23:24:10Z',\n",
        " 'id': 'fb1cfb04d3ef99d07c21f9dbf87ccc68',\n",
        " 'name': 'NA18948.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam',\n",
-       " 'self_url': 'drs://locate.md-be.ncbi.nlm.nih.gov/fb1cfb04d3ef99d07c21f9dbf87ccc68',\n",
+       " 'self_url': 'drs://locate.be-md.ncbi.nlm.nih.gov/fb1cfb04d3ef99d07c21f9dbf87ccc68',\n",
        " 'size': 8752606127}"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -216,15 +219,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "access_id:b5f46aadbcb48d7141104db0440feb63cd4e61c8\n",
-      "url:https://1000genomes.s3.amazonaws.com/phase3/data/NA18948/exome_alignment/NA18948.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam\n"
+      "access_id:1e4846c05c81a49f684e7f940ffbd3a98e5f0e335f019ee4d32d85c72096b743\n",
+      "url:https://storage.googleapis.com/genomics-public-data/ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA18948/exome_alignment/NA18948.mapped.ILLUMINA.bwa.JPT.exome.20121211.bam\n"
      ]
     }
    ],
@@ -250,14 +253,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Running FASPNotebook14-SRAExample.ipynb\n"
+      "Running /var/folders/wz/jjbxsnr13v7dkw2jkbpmqd_dly65gq/T/ipykernel_9333/2705327017.py\n"
      ]
     }
    ],
@@ -280,7 +283,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -289,15 +292,15 @@
      "text": [
       "subject=NA18948, drsID=fb1cfb04d3ef99d07c21f9dbf87ccc68\n",
       "https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1\n",
-      "Submitted run f5675d2a-4735-4076-b217-accdb6d20858 to sbcgcWESClient\n",
+      "Submitted run 3acc2387-904e-4310-b866-b8ca6e1dbeb2 to sbcgcWESClient\n",
       "_________________________________________________________________________\n",
       "subject=NA18945, drsID=9327fb44eb81b49a41e38c8d86eb3b3a\n",
       "https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1\n",
-      "Submitted run db841fd9-586e-4b9c-a3b4-e7d073dbb583 to sbcgcWESClient\n",
+      "Submitted run c697c9f9-5de7-4d11-89bb-d95ba27e4826 to sbcgcWESClient\n",
       "_________________________________________________________________________\n",
       "subject=NA18943, drsID=9f38253b281c7e9c99e4bdbececd8e2f\n",
       "https://cgc-ga4gh-api.sbgenomics.com/ga4gh/wes/v1\n",
-      "Submitted run bf37f355-4fc0-4684-810a-2e8954518e1a to sbcgcWESClient\n",
+      "Submitted run 637ca388-8127-4933-ac53-272e1abd995a to sbcgcWESClient\n",
       "_________________________________________________________________________\n"
      ]
     }
@@ -460,7 +463,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -474,7 +477,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.3"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Kids First Familial Leukemia - FHIR and DRS.ipynb b/notebooks/Kids First Familial Leukemia - FHIR and DRS.ipynb
@@ -16,7 +16,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,8 +25,8 @@
     "import json\n",
     "\n",
     "\n",
-    "endpoint = 'https://ncpi-api-fhir-service-dev.kidsfirstdrc.org'\n",
-    "full_cookie_path = os.path.expanduser('~/.keys/ncpi_fhir_cookie.json')\n",
+    "endpoint = 'https://kf-api-fhir-service.kidsfirstdrc.org'\n",
+    "full_cookie_path = os.path.expanduser('~/.keys/ncpi_prod_fhir_cookie.json')\n",
     "with open(full_cookie_path) as f:\n",
     "        cookies = json.load(f)\n",
     "\n",
@@ -35,14 +35,24 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "# of subjects found 577137:10\n"
+     "ename": "JSONDecodeError",
+     "evalue": "Expecting value: line 1 column 1 (char 0)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mJSONDecodeError\u001b[0m                           Traceback (most recent call last)",
+      "\u001b[0;32m/var/folders/wz/jjbxsnr13v7dkw2jkbpmqd_dly65gq/T/ipykernel_71789/1239882772.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mstudyid\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m577137\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mresources\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresources\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msearch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstudy\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstudyid\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlimit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m10\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0msubjects\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mresources\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfetch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      5\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"# of subjects found {}:{}\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstudyid\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msubjects\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0;31m#for s in subjects:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/imfenvs/fasp/lib/python3.9/site-packages/fhirpy/base/lib.py\u001b[0m in \u001b[0;36mfetch\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    139\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mSyncSearchSet\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mAbstractSearchSet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mABC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    140\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mfetch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 141\u001b[0;31m         bundle_data = self.client._fetch_resource(\n\u001b[0m\u001b[1;32m    142\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mresource_type\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    143\u001b[0m         )\n",
+      "\u001b[0;32m~/imfenvs/fasp/lib/python3.9/site-packages/fhirpy/base/lib.py\u001b[0m in \u001b[0;36m_fetch_resource\u001b[0;34m(self, path, params)\u001b[0m\n\u001b[1;32m    134\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    135\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_fetch_resource\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpath\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 136\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_do_request\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'get'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpath\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparams\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mparams\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    137\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    138\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/imfenvs/fasp/lib/python3.9/site-packages/fhirpy/base/lib.py\u001b[0m in \u001b[0;36m_do_request\u001b[0;34m(self, method, path, data, params)\u001b[0m\n\u001b[1;32m    124\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    125\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;36m200\u001b[0m \u001b[0;34m<=\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstatus_code\u001b[0m \u001b[0;34m<\u001b[0m \u001b[0;36m300\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 126\u001b[0;31m             return json.loads(\n\u001b[0m\u001b[1;32m    127\u001b[0m                 \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontent\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mobject_hook\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mAttrDict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    128\u001b[0m             ) if r.content else None\n",
+      "\u001b[0;32m~/.pyenv/versions/3.9.7/lib/python3.9/json/__init__.py\u001b[0m in \u001b[0;36mloads\u001b[0;34m(s, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)\u001b[0m\n\u001b[1;32m    357\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mparse_constant\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    358\u001b[0m         \u001b[0mkw\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'parse_constant'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparse_constant\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 359\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0mcls\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkw\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m~/.pyenv/versions/3.9.7/lib/python3.9/json/decoder.py\u001b[0m in \u001b[0;36mdecode\u001b[0;34m(self, s, _w)\u001b[0m\n\u001b[1;32m    335\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    336\u001b[0m         \"\"\"\n\u001b[0;32m--> 337\u001b[0;31m         \u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraw_decode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midx\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0m_w\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    338\u001b[0m         \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_w\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mend\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    339\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m!=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/.pyenv/versions/3.9.7/lib/python3.9/json/decoder.py\u001b[0m in \u001b[0;36mraw_decode\u001b[0;34m(self, s, idx)\u001b[0m\n\u001b[1;32m    353\u001b[0m             \u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscan_once\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    354\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mStopIteration\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 355\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mJSONDecodeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Expecting value\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    356\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mend\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mJSONDecodeError\u001b[0m: Expecting value: line 1 column 1 (char 0)"
      ]
     }
    ],
Original file line number	Diff line number	Diff line change
Expand Up		@@ -142,3 +142,4 @@ dmypy.json

		# Mac OS X
		.DS_Store
		*.dcm