diff --git a/.env-tpl b/.env-tpl index c215c39..2eb6280 100644 --- a/.env-tpl +++ b/.env-tpl @@ -1,5 +1,4 @@ -AIDBOX_LICENSE_ID= -AIDBOX_LICENSE_KEY= +AIDBOX_LICENSE= # comment to get unsecured box AIDBOX_CLIENT_ID=root diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..edbe261 --- /dev/null +++ b/.gitignore @@ -0,0 +1,5 @@ +.DS_Store +.idea +*.log +tmp/ +.env diff --git a/Lab #0. Data initialization.ipynb b/Lab #0. Data initialization.ipynb index db711bf..6216de9 100644 --- a/Lab #0. Data initialization.ipynb +++ b/Lab #0. Data initialization.ipynb @@ -61,7 +61,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -88,7 +88,7 @@ "outputs": [], "source": [ "dataset_path = './dataset'\n", - "import_dataset(client, './dataset')\n" + "await import_dataset(client, './dataset')" ] }, { @@ -111,7 +111,8 @@ "metadata": {}, "outputs": [], "source": [ - "client.resources('Patient').count()" + "resources = client.resources('Patient')\n", + "print(await resources.count())" ] }, { @@ -151,7 +152,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/Lab #1. Introduction to FHIR resources.ipynb b/Lab #1. Introduction to FHIR resources.ipynb index e70e13f..da1a22e 100644 --- a/Lab #1. Introduction to FHIR resources.ipynb +++ b/Lab #1. Introduction to FHIR resources.ipynb @@ -91,7 +91,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -143,7 +143,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').fetch_all()" + "patients = await client.resources('Patient').fetch_all()" ] }, { @@ -211,7 +211,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').sort('name').fetch_all()" + "patients = await client.resources('Patient').sort('name').fetch_all()" ] }, { @@ -271,7 +271,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').search(name=['John', 'Thompson']).fetch_all()\n", + "patients = await client.resources('Patient').search(name=['John', 'Thompson']).fetch_all()\n", "patients" ] }, @@ -289,7 +289,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').search(birthdate='1982-08-02').fetch_all()\n", + "patients = await client.resources('Patient').search(birthdate='1982-08-02').fetch_all()\n", "patients" ] }, @@ -306,7 +306,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').search(address='Philadelphia').fetch_all()\n", + "patients = await client.resources('Patient').search(address='Philadelphia').fetch_all()\n", "patients" ] }, @@ -339,7 +339,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient = client.resources('Patient').first()" + "patient = await client.resources('Patient').first()" ] }, { @@ -538,7 +538,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient.save()" + "await patient.save()" ] }, { @@ -630,7 +630,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient.save()" + "await patient.save()" ] }, { @@ -655,7 +655,7 @@ "metadata": {}, "outputs": [], "source": [ - "patients = client.resources('Patient').search(name=['John', 'Thompson']).fetch_all()\n", + "patients = await client.resources('Patient').search(name=['John', 'Thompson']).fetch_all()\n", "pprint(patients)" ] }, @@ -731,7 +731,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/Lab #2. Observation FHIR resource.ipynb b/Lab #2. Observation FHIR resource.ipynb index 28a300f..c9d8fa9 100644 --- a/Lab #2. Observation FHIR resource.ipynb +++ b/Lab #2. Observation FHIR resource.ipynb @@ -85,7 +85,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -135,7 +135,7 @@ "metadata": {}, "outputs": [], "source": [ - "observations = client.resources('Observation').limit(10).fetch()" + "observations = await client.resources('Observation').limit(10).fetch()" ] }, { @@ -289,7 +289,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient = client.resources('Patient').search(name=['John', 'Thompson']).first()\n", + "patient = await client.resources('Patient').search(name=['John', 'Thompson']).first()\n", "patient" ] }, @@ -315,7 +315,7 @@ "metadata": {}, "outputs": [], "source": [ - "observation.save()" + "await observation.save()" ] }, { @@ -383,7 +383,7 @@ "metadata": {}, "outputs": [], "source": [ - "weight_observation.save()" + "await weight_observation.save()" ] }, { @@ -455,7 +455,7 @@ "metadata": {}, "outputs": [], "source": [ - "blood_pressure_observation.save()" + "await blood_pressure_observation.save()" ] }, { @@ -520,7 +520,7 @@ "metadata": {}, "outputs": [], "source": [ - "client.resources('Observation').search(patient=patient['id']).fetch_all()" + "await client.resources('Observation').search(patient=patient['id']).fetch_all()" ] }, { @@ -543,7 +543,7 @@ "metadata": {}, "outputs": [], "source": [ - "client.resources('Patient').has('Observation', 'patient', code='8310-5').fetch_all()" + "await client.resources('Patient').has('Observation', 'patient', code='8310-5').fetch_all()" ] }, { @@ -608,7 +608,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/Lab #3. Practitioner and Schedule FHIR resources.ipynb b/Lab #3. Practitioner and Schedule FHIR resources.ipynb index f025b6c..fca5378 100644 --- a/Lab #3. Practitioner and Schedule FHIR resources.ipynb +++ b/Lab #3. Practitioner and Schedule FHIR resources.ipynb @@ -86,7 +86,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -210,7 +210,7 @@ "source": [ "Let's search for a schedule with `General Practice` type of appointments. \n", "\n", - "`Schedule` has a [search parameter](https://www.hl7.org/fhir/schedule.html#search) `type` that translates into `serviceType` field. `serviceType` is defined in terms of [ServiceType value set](https://www.hl7.org/fhir/valueset-service-type.html). \n", + "`Schedule` has a [search parameter](https://www.hl7.org/fhir/schedule.html#search) `service-type` that translates into `serviceType` field. `serviceType` is defined in terms of [ServiceType value set](https://www.hl7.org/fhir/valueset-service-type.html). \n", "On the value set `General Practice` is defined with code `124`.\n", "\n", "Note that every `Schedule` provides availability information for a list of resources. The list is stored in a field `actor`. \n", @@ -223,7 +223,7 @@ "metadata": {}, "outputs": [], "source": [ - "schedules = client.resources('Schedule').search(date='2018-09-16', type=124).include('Schedule', 'actor').fetch()\n", + "schedules = await client.resources('Schedule').search(**{'date': '2018-09-16', 'service-type': 124}).include('Schedule', 'actor').fetch()\n", "schedules" ] }, @@ -305,7 +305,7 @@ "metadata": {}, "outputs": [], "source": [ - "slots = client.resources('Slot').search(schedule=schedule['id']).fetch()\n", + "slots = await client.resources('Slot').search(schedule=schedule['id']).fetch()\n", "[(slot.get('start'), slot.get('end'), slot.get('status')) for slot in slots]" ] }, @@ -322,7 +322,7 @@ "metadata": {}, "outputs": [], "source": [ - "slots = client.resources('Slot').search(\n", + "slots = await client.resources('Slot').search(\n", " schedule=schedule['id'],\n", " # Write code here\n", ").fetch()\n", @@ -342,7 +342,7 @@ "metadata": {}, "outputs": [], "source": [ - "slots = client.resources('Slot').search(\n", + "slots = await client.resources('Slot').search(\n", " schedule=schedule['id'],\n", " # Write code here\n", ").fetch()\n", @@ -404,7 +404,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/Lab #4. Appointment FHIR resource.ipynb b/Lab #4. Appointment FHIR resource.ipynb index 7806cc8..70d0923 100644 --- a/Lab #4. Appointment FHIR resource.ipynb +++ b/Lab #4. Appointment FHIR resource.ipynb @@ -84,7 +84,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -116,7 +116,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient = client.resources('Patient').search(name=['John', 'Thompson']).first()\n", + "patient = await client.resources('Patient').search(name=['John', 'Thompson']).first()\n", "patient" ] }, @@ -133,7 +133,7 @@ "metadata": {}, "outputs": [], "source": [ - "practitioner = client.resources('Practitioner').search(\n", + "practitioner = await client.resources('Practitioner').search(\n", " # Write code here\n", ").first()\n", "practitioner" @@ -159,7 +159,7 @@ "metadata": {}, "outputs": [], "source": [ - "schedule = client.resources('Schedule').search(\n", + "schedule = await client.resources('Schedule').search(\n", " # Write code here\n", ").first()\n", "schedule" @@ -178,7 +178,7 @@ "metadata": {}, "outputs": [], "source": [ - "slot = client.resources('Slot').search(\n", + "slot = await client.resources('Slot').search(\n", " schedule=schedule['id'],\n", " # Write code here\n", ").first()\n", @@ -199,7 +199,7 @@ "outputs": [], "source": [ "slot['status'] = 'busy'\n", - "slot.save()" + "await slot.save()" ] }, { @@ -258,7 +258,7 @@ " slot=[slot],\n", " participant=participants\n", ")\n", - "appointment.save()\n", + "await appointment.save()\n", "\n", "pprint(appointment)" ] @@ -283,7 +283,7 @@ "metadata": {}, "outputs": [], "source": [ - "appointments = client.resources('Appointment').search(\n", + "appointments = await client.resources('Appointment').search(\n", " # Write code here\n", ").fetch()\n", "[(ap.get('start'), ap.get('end'), ap.get('status')) for ap in appointments]" @@ -343,7 +343,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/Lab #5. Encounter FHIR resource.ipynb b/Lab #5. Encounter FHIR resource.ipynb index dffdf38..fa9ad6f 100644 --- a/Lab #5. Encounter FHIR resource.ipynb +++ b/Lab #5. Encounter FHIR resource.ipynb @@ -89,7 +89,7 @@ "metadata": {}, "outputs": [], "source": [ - "client = fhirpy.FHIRClient(\n", + "client = fhirpy.AsyncFHIRClient(\n", " url=os.environ['BOX_URL'] + '/fhir', \n", " authorization=os.environ['BOX_AUTHORIZATION'])" ] @@ -121,7 +121,7 @@ "metadata": {}, "outputs": [], "source": [ - "patient = client.resources('Patient').search(\n", + "patient = await client.resources('Patient').search(\n", " # Write code here\n", ").first()\n", "patient" @@ -140,7 +140,7 @@ "metadata": {}, "outputs": [], "source": [ - "practitioner = client.resources('Practitioner').search(\n", + "practitioner = await client.resources('Practitioner').search(\n", " # Write code here\n", ").first()\n", "practitioner" @@ -161,7 +161,7 @@ "metadata": {}, "outputs": [], "source": [ - "location = client.resources('Location').search(\n", + "location = await client.resources('Location').search(\n", " # Write code here\n", ").first()\n", "location" @@ -180,7 +180,7 @@ "metadata": {}, "outputs": [], "source": [ - "appointment = client.resources('Appointment').search(actor=patient['id']).first()\n", + "appointment = await client.resources('Appointment').search(actor=patient['id']).first()\n", "appointment" ] }, @@ -226,7 +226,7 @@ "metadata": {}, "outputs": [], "source": [ - "encounters = client.resources('Encounter').search(subject=patient['id']).first()\n", + "encounters = await client.resources('Encounter').search(subject=patient['id']).first()\n", "encounters" ] }, @@ -434,7 +434,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.7.3" } }, "nbformat": 4, diff --git a/README.md b/README.md index 0d202f9..24a5df3 100644 --- a/README.md +++ b/README.md @@ -40,9 +40,9 @@ mv .env-tpl .env ## License obtaining -Before you start you have to get free development license keys. Please [follow this instructions](https://docs.aidbox.app/installation/setup-aidbox.dev#license-obtaining). +Before you start you have to get an Aidbox license. Please [follow this instructions](https://docs.aidbox.app/getting-started/run-aidbox-locally-with-docker#get-a-license). -Then add your License id and License key to the env file. +Then add your License to the env file. ![.env file](images/dotenv_license_key.png) @@ -61,18 +61,14 @@ After devbox-db and devbox started and initialized, you can go to http://127.0.0 It is a main screen of jupyter web interface. Now you need to clone the current repository using the terminal. Click the 'New' button as it shown on the screen below, and select 'Terminal'. -![Jupyter terminal](images/jupyter_create_terminal.png) +![Jupyter terminal](images/jupyter_create_terminal_1.png) The new terminal window will be opened. -![Jupyter terminal](images/terminal.png) - This terminal provides the full access to the file system. Input the next commands into the terminal to update the `fhirpy` library and clone the repository: ``` -pip install --upgrade fhirpy -``` +pip install --upgrade git+https://github.com/beda-software/fhir-py.git -``` git clone https://github.com/Aidbox/jupyter-course ``` @@ -80,8 +76,6 @@ git clone https://github.com/Aidbox/jupyter-course Go back to the jupyter web interface. Now you can see a just cloned directory 'jupyter-course'. -![Jupyter](images/jupyter_with_repo.png) - Click the 'jupyter-course' directory to open it. ![Jupyter](images/jupyter_courses.png) @@ -92,12 +86,11 @@ The directory contains this instruction and laboratory works. Before you start d Click 'Lab #0. Data initialization.ipynb' to open an initial notebook. -![Jupyter Notebook](images/jupyter_notebook_init.png) Run this notebook step-by-step using 'Run' command from toolbar. As a result, you should get the same messages as on the screen below. -![Jupyter Notebook](images/jupyter_notebook_import_results.png) +![Jupyter Notebook](images/jupyter_notebook_first.png) If you see an error message or zero patients imported, contact the support team support@health-samurai.io for help. Also, don't try to run this notebook again, you will always get an error. @@ -106,7 +99,7 @@ In other cases, you are ready to start doing laboratory works. Start from the first 'Lab #1. Introduction to FHIR resources.ipynb' Good luck! -![Jupyter Notebook](images/jupyter_notebook_first.png) + # Support @@ -117,11 +110,8 @@ If you have any questions about the laboratory works, please create an issue in If you like the laboratory works and would like to keep learning, we are happy to prepare more new laboratory works. Please, visit our github and star our tools: -https://github.com/beda-software/tk3 https://github.com/beda-software/fhir-py -Once both repositories get 100 stars, we'll share the next two laboratory works about Machine Learning and Data Analysis for FHIR. - # Authors -(c) 2018 Beda.Software, Health Samurai +(c) 2022 Beda.Software, Health Samurai diff --git a/dataset/initial_data.json b/dataset/initial_data.json index 8b51947..bcb4469 100644 --- a/dataset/initial_data.json +++ b/dataset/initial_data.json @@ -1 +1,787 @@ -{"resourceType": "Bundle", "type": "transaction", "entry": [{"resource": {"id": "hahnemann", "name": "Hahnemann University Hospital", "address": {"state": "Pennsylvania", "country": "USA", "city": "Philadelphia", "postalCode": "19102", "line": ["230 N Broad St"], "text": "230 N Broad St, Philadelphia, PA 19102, USA"}, "resourceType": "Location", "meta": {"lastUpdated": "2018-11-02T05:54:11.252Z", "versionId": "64", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Location"}}, {"resource": {"id": "practitioner_kelly_smith", "name": [{"given": ["Kelly"], "family": "Smith", "text": "Kelly Smith"}], "qualification": [{"code": {"coding": [{"system": "http://hl7.org/fhir/v2/0360/2.7", "code": "PHD"}]}}], "resourceType": "Practitioner", "meta": {"lastUpdated": "2018-11-02T05:54:11.308Z", "versionId": "65", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Practitioner"}}, {"resource": {"id": "practitioner_adam_ainsley", "name": [{"given": ["Adam"], "family": "Ainsley", "text": "Adam Ainsley"}], "qualification": [{"code": {"coding": [{"system": "http://hl7.org/fhir/v2/0360/2.7", "code": "PHD"}]}}], "resourceType": "Practitioner", "meta": {"lastUpdated": "2018-11-02T05:54:11.363Z", "versionId": "66", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Practitioner"}}, {"resource": {"id": "practitioner_robert_alby", "name": [{"given": ["Robert"], "family": "Alby", "text": "Robert Alby"}], "qualification": [{"code": {"coding": [{"system": "http://hl7.org/fhir/v2/0360/2.7", "code": "PHD"}]}}], "resourceType": "Practitioner", "meta": {"lastUpdated": "2018-11-02T05:54:11.421Z", "versionId": "67", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Practitioner"}}, {"resource": {"id": "practitioner_role_kelly_smith", "practitioner": {"reference": "Practitioner/practitioner_kelly_smith"}, "location": [{"reference": "Location/hahnemann"}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "resourceType": "PractitionerRole", "meta": {"lastUpdated": "2018-11-02T05:54:11.540Z", "versionId": "68", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "PractitionerRole"}}, {"resource": {"id": "practitioner_role_adam_ainsley", "practitioner": {"reference": "Practitioner/practitioner_adam_ainsley"}, "location": [{"reference": "Location/hahnemann"}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "resourceType": "PractitionerRole", "meta": {"lastUpdated": "2018-11-02T05:54:11.598Z", "versionId": "69", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "PractitionerRole"}}, {"resource": {"id": "practitioner_role_robert_alby", "practitioner": {"reference": "Practitioner/practitioner_robert_alby"}, "location": [{"reference": "Location/hahnemann"}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "resourceType": "PractitionerRole", "meta": {"lastUpdated": "2018-11-02T05:54:11.655Z", "versionId": "70", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "PractitionerRole"}}, {"resource": {"id": "schedule_for_kelly_smith", "active": true, "serviceCategory": {"coding": [{"code": "17", "display": "General Practice"}]}, "serviceType": [{"coding": [{"code": "124", "display": "General Practice"}]}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "actor": [{"reference": "Practitioner/practitioner_kelly_smith", "display": "Kelly Smith"}, {"reference": "Location/hahnemann", "display": "Hahnemann University Hospital"}], "planningHorizon": {"start": "2018-09-16T09:00:00Z", "end": "2018-09-16T18:00:00Z"}, "resourceType": "Schedule", "meta": {"lastUpdated": "2018-11-02T05:54:11.712Z", "versionId": "71", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Schedule"}}, {"resource": {"id": "slot_for_schedule_for_kelly_smith_0", "start": "2018-09-16T09:00:00", "end": "2018-09-16T10:00:00", "status": "free", "schedule": {"reference": "Schedule/schedule_for_kelly_smith"}, "serviceCategory": {"coding": [{"code": "17", "display": "General Practice"}]}, "serviceType": [{"coding": [{"code": "124", "display": "General Practice"}]}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "resourceType": "Slot", "meta": {"lastUpdated": "2018-11-02T05:54:11.768Z", "versionId": "72", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": "POST", "url": "Slot"}}, {"resource": {"id": "slot_for_schedule_for_kelly_smith_1", "start": "2018-09-16T10:00:00", "end": "2018-09-16T11:00:00", "status": "free", "schedule": {"reference": "Schedule/schedule_for_kelly_smith"}, "serviceCategory": {"coding": [{"code": "17", "display": "General Practice"}]}, "serviceType": [{"coding": [{"code": "124", "display": "General Practice"}]}], "specialty": [{"coding": [{"code": "394814009", "display": "General Practice"}]}], "resourceType": "Slot", "meta": {"lastUpdated": "2018-11-02T05:54:11.824Z", "versionId": "73", "tag": [{"system": "https://aidbox.app", "code": "created"}]}}, "request": {"method": 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Care Plan for Fracture care.
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Care Plan for Physical therapy procedure.
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"request": { + "method": "PUT", + "url": "Claim/af4861ce-b7b5-4621-9d4a-44f904edaf50" + } + }, + { + "fullUrl": "urn:uuid:8f6f839d-d958-4170-bfdc-0c8933fe76a4", + "resource": { + "resourceType": "ExplanationOfBenefit", + "id": "8f6f839d-d958-4170-bfdc-0c8933fe76a4", + "contained": [ + { + "resourceType": "ServiceRequest", + "id": "referral", + "status": "completed", + "intent": "order", + "subject": { + "reference": "urn:uuid:0ed60bfc-7efc-410d-ba43-2ac270115582" + }, + "requester": { + "reference": "urn:uuid:0000016e-3ee4-e934-0000-0000000000b4" + }, + "performer": [ + { + "reference": "urn:uuid:0000016e-3ee4-e934-0000-0000000000b4" + } + ] + }, + { + "resourceType": "Coverage", + "id": "coverage", + "status": "active", + "type": { + "text": "Aetna" + }, + "beneficiary": { + "reference": "urn:uuid:0ed60bfc-7efc-410d-ba43-2ac270115582" + }, + "payor": [ + { + "display": "Aetna" + } + ] + } + ], + "identifier": [ + { + "system": "https://bluebutton.cms.gov/resources/variables/clm_id", + "value": "af4861ce-b7b5-4621-9d4a-44f904edaf50" + }, + { + "system": "https://bluebutton.cms.gov/resources/identifier/claim-group", + "value": "99999999999" + } + ], + "status": "active", + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/claim-type", + "code": "institutional" + } + ] + }, + "use": "claim", + "patient": { + "reference": "urn:uuid:0ed60bfc-7efc-410d-ba43-2ac270115582" + }, + "billablePeriod": { + "start": "2019-07-16T19:53:27+07:00", + "end": "2020-07-16T19:53:27+07:00" + }, + "created": "2019-07-16T19:53:27+07:00", + "insurer": { + "display": "Aetna" + }, + "provider": { + "reference": "urn:uuid:0000016e-3ee4-e934-0000-0000000000b4" + }, + "referral": { + "reference": "#referral" + }, + "claim": { + "reference": "urn:uuid:af4861ce-b7b5-4621-9d4a-44f904edaf50" + }, + "outcome": "complete", + "careTeam": [ + { + "sequence": 1, + "provider": { + "reference": "urn:uuid:0000016e-3ee4-e934-0000-0000000000b4" + }, + "role": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/claimcareteamrole", + "code": "primary", + "display": "Primary Care Practitioner" + } + ] + } + } + ], + "diagnosis": [ + { + "sequence": 1, + "diagnosisReference": { + "reference": "urn:uuid:e5e21e27-5be9-480c-b70d-bdb521ee3341" + }, + "type": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/ex-diagnosistype", + "code": "principal" + } + ] + } + ] + } + ], + "insurance": [ + { + "focal": true, + "coverage": { + "reference": "#coverage", + "display": "Aetna" + } + } + ], + "item": [ + { + "sequence": 1, + "category": { + "coding": [ + { + "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd", + "code": "1", + "display": "Medical care" + } + ] + }, + "productOrService": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "185345009", + "display": "Encounter for symptom" + } + ], + "text": "Encounter for symptom" + }, + "servicedPeriod": { + "start": "2019-07-16T19:38:27+07:00", + "end": "2019-07-16T19:53:27+07:00" + }, + "locationCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace", + "code": "21", + "display": "Inpatient Hospital" + } + ] + }, + "encounter": [ + { + "reference": "urn:uuid:cfe20845-ac9e-4799-95c9-60ba890420ed" + } + ] + }, + { + "sequence": 2, + "diagnosisSequence": [ + 1 + ], + "category": { + "coding": [ + { + "system": "https://bluebutton.cms.gov/resources/variables/line_cms_type_srvc_cd", + "code": "1", + "display": "Medical care" + } + ] + }, + "productOrService": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "195662009", + "display": "Acute viral pharyngitis (disorder)" + } + ], + "text": "Acute viral pharyngitis (disorder)" + }, + "servicedPeriod": { + "start": "2019-07-16T19:38:27+07:00", + "end": "2019-07-16T19:53:27+07:00" + }, + "locationCodeableConcept": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/ex-serviceplace", + "code": "21", + "display": "Inpatient Hospital" + } + ] + } + } + ], + "total": [ + { + "category": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/adjudication", + "code": "submitted", + "display": "Submitted Amount" + } + ], + "text": "Submitted Amount" + }, + "amount": { + "value": 129.16, + "currency": "USD" + } + } + ], + "payment": { + "amount": { + "value": 0, + "currency": "USD" + } + } + }, + "request": { + "method": "PUT", + "url": "ExplanationOfBenefit/8f6f839d-d958-4170-bfdc-0c8933fe76a4" + } + } + ] +} diff --git a/docker-compose.yaml b/docker-compose.yaml index 803f866..6aade55 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -1,7 +1,7 @@ version: '3.1' services: devbox: - image: "healthsamurai/devbox:0.4.7" + image: "healthsamurai/aidboxone:edge" command: ["wait-for-it.sh", "devbox-db:5432", "--strict", "--timeout=0", "--", "java", "-jar", "/aidbox.jar", "-m", "devbox.core"] depends_on: - devbox-db @@ -24,7 +24,7 @@ services: - ./wait-for-it.sh:/usr/local/bin/wait-for-it.sh - ./config:/var/config devbox-db: - image: "aidbox/db:11.4.0.2" + image: "healthsamurai/aidboxdb:14.2" expose: - 5432 environment: @@ -32,7 +32,7 @@ services: POSTGRES_PASSWORD: postgres POSTGRES_DB: devbox jupyter-course: - image: jupyter/datascience-notebook + image: jupyter/minimal-notebook ports: - 8888:8888 depends_on: diff --git a/images/dotenv_license_key.png b/images/dotenv_license_key.png index 2782215..33b72c6 100644 Binary files a/images/dotenv_license_key.png and b/images/dotenv_license_key.png differ diff --git a/images/jupyter.png b/images/jupyter.png index 544996e..114cafc 100644 Binary files a/images/jupyter.png and b/images/jupyter.png differ diff --git a/images/jupyter_courses.png b/images/jupyter_courses.png index 58b4651..65523b5 100644 Binary files a/images/jupyter_courses.png and b/images/jupyter_courses.png differ diff --git a/images/jupyter_create_terminal.png b/images/jupyter_create_terminal.png deleted file mode 100644 index ecef033..0000000 Binary files a/images/jupyter_create_terminal.png and /dev/null differ diff --git a/images/jupyter_create_terminal_1.png b/images/jupyter_create_terminal_1.png new file mode 100644 index 0000000..b2e731e Binary files /dev/null and b/images/jupyter_create_terminal_1.png differ diff --git a/images/jupyter_notebook_first.png b/images/jupyter_notebook_first.png index 5222c21..b95afa0 100644 Binary files a/images/jupyter_notebook_first.png and b/images/jupyter_notebook_first.png differ diff --git a/images/terminal.png b/images/terminal.png deleted file mode 100644 index 38b79b4..0000000 Binary files a/images/terminal.png and /dev/null differ diff --git a/images/terminal_git_clone.png b/images/terminal_git_clone.png index 8251a4a..6445073 100644 Binary files a/images/terminal_git_clone.png and b/images/terminal_git_clone.png differ diff --git a/initialize.py b/initialize.py index 55653e7..4569f55 100644 --- a/initialize.py +++ b/initialize.py @@ -4,17 +4,16 @@ import os.path -def import_bundle(client, filename): +async def import_bundle(client, filename): with open(filename) as fd: patient_json = json.load(fd) bundle = client.resource('Bundle') bundle['type'] = 'transaction' - bundle._get_path = lambda: '' bundle['entry'] = patient_json['entry'] - bundle.save() + await bundle.save() -def import_dataset(client, dataset_path): +async def import_dataset(client, dataset_path): sys.stdout.write("Import progress: 0% \r") filenames = [ @@ -23,10 +22,9 @@ def import_dataset(client, dataset_path): total_count = len(filenames) for index, filename in enumerate(filenames): - import_bundle(client, os.path.join(dataset_path, filename)) + await import_bundle(client, os.path.join(dataset_path, filename)) progress = int(float(index + 1) / float(total_count) * 100) sys.stdout.write("Import progress: %d%% \r" % progress) sys.stdout.flush() sys.stdout.write("Import progress: 100%\n") sys.stdout.write("{0} bundles imported".format(total_count)) -