Adds case study notebooks

case_studies/case-study-kids-first-README.ipynb

@@ -0,0 +1,101 @@
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+    "## Data retrieval\n",
+    "\n",
+    "### From kids first\n",
+    "\n",
+    "\n",
+    "For each study:\n",
+    "* SD_DYPMEHHF\n",
+    "* SD_8Y99QZJJ\n",
+    "* SD_PET7Q6F2\n",
+    "\n",
+    "\n",
+    "\n",
+    "e.g.: \n",
+    "\n",
+    "\n",
+    "```\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/ResearchSubject?_tag=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] | .resource' > ResearchSubject.ndjson\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/Patient?_tag=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] | .resource' > Patient.ndjson\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/Specimen?_tag=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] | .resource' > Specimen.ndjson\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/DocumentReference?_tag=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] | .resource' > DocumentReference.ndjson\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/Observation?_tag=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] |.resource' > Observation.ndjson\n",
+    "kf_curl \"https://kf-api-fhir-service.kidsfirstdrc.org/ResearchStudy?identifier=SD_DYPMEHHF&_count=1000\" | jq -c '.entry[] | .resource' > ResearchStudy.ndjson\n",
+    "```\n",
+    "\n",
+    "See https://github.com/bmeg/fhir-workshop#data-retrieval for more on kf_curl\n",
+    "\n",
+    "\n",
+    "\n",
+    "To install:\n",
+    "\n",
+    "* from `open terminal` window\n",
+    "\n",
+    "\n",
+    "```\n",
+    "git clone https://github.com/bmeg/fhir-workshop\n",
+    "cd fhir-workshop\n",
+    "pip install -e . \n",
+    "```\n",
+    "\n",
+    "\n",
+    "\n",
+    "\n",
+    "### From workspace bucket \n",
+    "\n",
+    "from `open terminal` window\n",
+    "\n",
+    "```\n",
+    "cd /home/jupyter/NCPI FHIR CAT 2022 - Working Space/edit\n",
+    "gsutil -m cp -r  $WORKSPACE_BUCKET/kids_first .\n",
+    "```"
+   ]
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