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slibby/DHIS2 example.ipynb

Created August 26, 2020 15:36
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Example Jupyter Notebook accessing indicators from the DHIS2 Test Site
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DHIS2 example.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<dhis2.api.Api at 0x2033053cac8>"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from dhis2 import Api\n",
"api = Api('https://covid19.dhis2.org/demo/', 'COVID', 'StopCovid19!')\n",
"api"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"r = api.get('schemas')\n",
"schemas = r.json()"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"attributes : /attributes\n",
"userRoles : /userRoles\n",
"users : /users\n",
"userGroups : /userGroups\n",
"externalFileResources : /externalFileResources\n",
"expressions : /expressions\n",
"sqlViews : /sqlViews\n",
"oAuth2Clients : /oAuth2Clients\n",
"constants : /constants\n",
"options : /options\n",
"jobConfigurations : /jobConfigurations\n",
"optionSets : /optionSets\n",
"optionGroupSets : /optionGroupSets\n",
"optionGroups : /optionGroups\n",
"colorSets : /colorSets\n",
"legendSets : /legendSets\n",
"organisationUnits : /organisationUnits\n",
"organisationUnitLevels : /organisationUnitLevels\n",
"organisationUnitGroups : /organisationUnitGroups\n",
"organisationUnitGroupSets : /organisationUnitGroupSets\n",
"categoryOptions : /categoryOptions\n",
"categoryOptionGroups : /categoryOptionGroups\n",
"categoryOptionGroupSets : /categoryOptionGroupSets\n",
"categories : /categories\n",
"categoryCombos : /categoryCombos\n",
"categoryOptionCombos : /categoryOptionCombos\n",
"dataElements : /dataElements\n",
"dataElementGroups : /dataElementGroups\n",
"dataElementGroupSets : /dataElementGroupSets\n",
"analyticsTableHooks : /analyticsTableHooks\n",
"indicatorTypes : /indicatorTypes\n",
"indicators : /indicators\n",
"indicatorGroups : /indicatorGroups\n",
"indicatorGroupSets : /indicatorGroupSets\n",
"dataEntryForms : /dataEntryForms\n",
"dataSets : /dataSets\n",
"dataSetNotificationTemplates : /dataSetNotificationTemplates\n",
"sections : /sections\n",
"dataApprovalLevels : /dataApprovalLevels\n",
"dataApprovalWorkflows : /dataApprovalWorkflows\n",
"validationRules : /validationRules\n",
"validationRuleGroups : /validationRuleGroups\n",
"validationNotificationTemplates : /validationNotificationTemplates\n",
"trackedEntityAttributes : /trackedEntityAttributes\n",
"trackedEntityTypes : /trackedEntityTypes\n",
"programTrackedEntityAttributeGroups : /programTrackedEntityAttributeGroups\n",
"programStageSections : /programStageSections\n",
"programNotificationTemplates : /programNotificationTemplates\n",
"smsCommands : /smsCommands\n",
"programStages : /programStages\n",
"programs : /programs\n",
"eventReports : /eventReports\n",
"eventCharts : /eventCharts\n",
"programSections : /programSections\n",
"programIndicators : /programIndicators\n",
"programIndicatorGroups : /programIndicatorGroups\n",
"programRuleVariables : /programRuleVariables\n",
"relationshipTypes : /relationshipTypes\n",
"programRuleActions : /programRuleActions\n",
"programRules : /programRules\n",
"mapViews : /mapViews\n",
"documents : /documents\n",
"validationResults : /validationResults\n",
"maps : /maps\n",
"charts : /charts\n",
"reportTables : /reportTables\n",
"reports : /reports\n",
"externalMapLayers : /externalMapLayers\n",
"predictors : /predictors\n",
"predictorGroups : /predictorGroups\n",
"dashboardItems : /dashboardItems\n",
"dashboards : /dashboards\n",
"pushAnalysis : /pushAnalysis\n",
"dataStores : /dataStore\n",
"fileResources : /fileResources\n",
"eventFilters : /eventFilters\n",
"trackedEntityAttributeValues : /trackedEntityAttributeValues\n",
"minMaxDataElements : /minMaxDataElements\n",
"programStageInstances : /programStageInstances\n",
"icons : /icons\n",
"messageConversations : /messageConversations\n",
"metadataVersions : /metadata/version\n",
"programDataElements : /programDataElements\n",
"interpretations : /interpretations\n",
"trackedEntityInstances : /trackedEntityInstances\n",
"programInstances : /programInstances\n",
"relationships : /relationships\n",
"dataElementOperands : /dataElementOperands\n"
]
}
],
"source": [
"for i in schemas['schemas']:\n",
" try:\n",
" print(i['collectionName'], \": \", i['relativeApiEndpoint'])\n",
" except:\n",
" pass"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'pager': {'page': 1, 'pageCount': 1, 'total': 22, 'pageSize': 50},\n",
" 'indicators': [{'id': 'jPRgGRxHfPa',\n",
" 'displayName': 'CHECK_COVID-19 Cases (events) - Case fatality rate (%)'},\n",
" {'id': 'adeOuUvQAtC', 'displayName': 'CHECK_COVID-2019 Case fatality rate'},\n",
" {'id': 'zUcGi0Y384Y', 'displayName': 'COVID-19 - Active cases'},\n",
" {'id': 'kJoSHTinHGa', 'displayName': 'COVID-19 - All cases'},\n",
" {'id': 'dXAhOKiim1x', 'displayName': 'COVID-19 - Case Fatality rate (%)'},\n",
" {'id': 'fK1b7O6CuBV',\n",
" 'displayName': 'COVID-19 - Cases treated by mechanical ventilation, ECMO or ICU'},\n",
" {'id': 'S3Ty19GEaqn', 'displayName': 'COVID-19 - Closed cases'},\n",
" {'id': 'ocBlGrHZy6Q', 'displayName': 'COVID-19 - Confirmed cases'},\n",
" {'id': 'zozhRzInMZm',\n",
" 'displayName': 'COVID-19 - Confirmed cases by Transmission Classification'},\n",
" {'id': 'r2VxAVW1IEy', 'displayName': 'COVID-19 - Deaths'},\n",
" {'id': 'BmW2IAaxIBe', 'displayName': 'COVID-19 - Hospitalised Cases'},\n",
" {'id': 'DSQpsxxxWSq',\n",
" 'displayName': 'COVID-19 POE - Travellers that developed symptoms within the 14 days period of follow-up (%)'},\n",
" {'id': 'jHzx1zXeHzV',\n",
" 'displayName': 'COVID-19 - Proportion of males among confirmed cases (%)'},\n",
" {'id': 'UF7s1t1v6KG',\n",
" 'displayName': 'COVID-19 - Proportion of males among deaths(%)'},\n",
" {'id': 'gYt2GEAdCJK',\n",
" 'displayName': 'COVID-19 - Provinces/regions with Transmission pattern (Cluster cases)'},\n",
" {'id': 'JpRDu51rbg5',\n",
" 'displayName': 'COVID-19 - Provinces/regions with Transmission pattern (Community cases)'},\n",
" {'id': 'vECy4BgZqRF',\n",
" 'displayName': 'COVID-19 - Provinces/regions with Transmission pattern (No cases)'},\n",
" {'id': 'GszrLGBvHhg',\n",
" 'displayName': 'COVID-19 - Provinces/regions with Transmission pattern (Sporadic cases)'},\n",
" {'id': 'PkGdfHQyWWH', 'displayName': 'COVID-19 - Recovered cases'},\n",
" {'id': 'dsho3rAaUkr', 'displayName': 'COVID-19 - Recovery rate (%)'},\n",
" {'id': 'v1xKfNthU2y', 'displayName': 'COVID-2019 Female Case fatality rate'},\n",
" {'id': 'n87hWfKcfWL', 'displayName': 'COVID-2019 Male Case fatality rate'}]}"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r = api.get('indicators')\n",
"r.json()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'lastUpdated': '2020-03-27T10:44:08.022',\n",
" 'id': 'PkGdfHQyWWH',\n",
" 'href': 'https://covid19.dhis2.org/demo/api/indicators/PkGdfHQyWWH',\n",
" 'created': '2020-03-18T09:46:52.459',\n",
" 'name': 'COVID-19 - Recovered cases',\n",
" 'shortName': 'Recovered cases',\n",
" 'displayName': 'COVID-19 - Recovered cases',\n",
" 'publicAccess': 'r-------',\n",
" 'displayShortName': 'Recovered cases',\n",
" 'externalAccess': False,\n",
" 'denominatorDescription': '1',\n",
" 'numeratorDescription': 'Number of cases that are recovered.',\n",
" 'dimensionItem': 'PkGdfHQyWWH',\n",
" 'numerator': '#{rvYTAOrBrtY}',\n",
" 'denominator': '1',\n",
" 'annualized': False,\n",
" 'favorite': False,\n",
" 'dimensionItemType': 'INDICATOR',\n",
" 'access': {'read': True,\n",
" 'update': False,\n",
" 'externalize': False,\n",
" 'delete': False,\n",
" 'write': False,\n",
" 'manage': False},\n",
" 'indicatorType': {'id': 'kHy61PbChXr'},\n",
" 'lastUpdatedBy': {'id': 'M2foyBloz3g'},\n",
" 'user': {'id': 'vUeLeQMSwhN'},\n",
" 'favorites': [],\n",
" 'translations': [{'property': 'NAME',\n",
" 'locale': 'fr',\n",
" 'value': 'COVID-19 - Affaires recouvrées'},\n",
" {'property': 'NAME', 'locale': 'en', 'value': 'COVID-19 - Recovered cases'},\n",
" {'property': 'NAME',\n",
" 'locale': 'es',\n",
" 'value': 'COVID-19 - Casos recuperados'},\n",
" {'property': 'SHORT_NAME', 'locale': 'en', 'value': 'Recovered cases'},\n",
" {'property': 'NAME',\n",
" 'locale': 'ru',\n",
" 'value': 'COVID-19 - Выздоровевшие случаи'},\n",
" {'property': 'SHORT_NAME', 'locale': 'es', 'value': 'Casos recuperados'},\n",
" {'property': 'SHORT_NAME', 'locale': 'fr', 'value': 'Cas guéris'},\n",
" {'property': 'NAME',\n",
" 'locale': 'pt',\n",
" 'value': 'COVID-19 - Casos Recuperados'}],\n",
" 'userGroupAccesses': [{'access': 'rw------',\n",
" 'userGroupUid': 'w4iJeNKy9br',\n",
" 'displayName': 'COVID19 admin',\n",
" 'id': 'w4iJeNKy9br'},\n",
" {'access': 'r-------',\n",
" 'userGroupUid': 'DoYehxUvmwT',\n",
" 'displayName': 'COVID19 access',\n",
" 'id': 'DoYehxUvmwT'}],\n",
" 'attributeValues': [],\n",
" 'indicatorGroups': [{'id': 'YKyPfpFUAVo'}],\n",
" 'userAccesses': [],\n",
" 'dataSets': [],\n",
" 'legendSets': []}"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r = api.get('indicators/PkGdfHQyWWH')\n",
"#r = api.get('dataValueSets')\n",
"r.json()"
]
},
{
"cell_type": "code",
"execution_count": 44,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Animal Region\n",
"[[[[164.6574,-67.6118],[164.7199,-67.6003],[164.7708,-67.6055],[164.7385,-67.6239],[164.7174,-67.6316],[164.6554,-67.6305],[164.6339,-67.625],[164.6574,-67.6118]]]]\n",
"Animal Region\n",
"[[[[164.6183,-67.51],[164.7239,-67.5099],[164.7206,-67.6002],[164.6574,-67.6117],[164.6591,-67.601],[164.656,-67.5903],[164.6116,-67.576],[164.6299,-67.5347],[164.6183,-67.51]]]]\n",
"Animal Region\n",
"[[[[164.5519,-67.5735],[164.5844,-67.5728],[164.6119,-67.5759],[164.656,-67.5904],[164.6591,-67.601],[164.6574,-67.612],[164.6339,-67.625],[164.6184,-67.6211],[164.6074,-67.6159],[164.6203,-67.6071],[164.6093,-67.5972],[164.5929,-67.592],[164.5686,-67.5925],[164.5607,-67.5866],[164.5566,-67.5803],[164.5519,-67.5735]]]]\n",
"Animal Region\n",
"[[[[164.5686,-67.5925],[164.5925,-67.592],[164.6095,-67.5973],[164.6205,-67.6071],[164.6074,-67.6159],[164.5872,-67.6065],[164.5805,-67.6014],[164.5686,-67.5925]]]]\n",
"Animal Region\n",
"[[[[164.6183,-67.51],[164.6299,-67.5347],[164.621,-67.5554],[164.6116,-67.576],[164.5846,-67.5726],[164.5519,-67.5735],[164.5378,-67.5524],[164.5328,-67.5205],[164.5148,-67.5097],[164.6183,-67.51]]]]\n",
"Animal Region\n",
"[[[[164.7706,-67.6056],[164.7213,-67.6005],[164.7213,-67.6003],[164.7239,-67.5099],[164.7903,-67.5091],[164.8237,-67.5516],[164.8258,-67.5705],[164.8106,-67.5826],[164.7706,-67.6056]]]]\n",
"Food Region\n",
"[[[[164.6982,-67.4731],[164.6376,-67.4493],[164.6394,-67.4412],[164.6342,-67.4358],[164.621,-67.4318],[164.612,-67.4314],[164.5999,-67.3461],[164.6185,-67.3469],[164.6529,-67.3578],[164.6796,-67.376],[164.675,-67.3973],[164.7151,-67.431],[164.6925,-67.4468],[164.6982,-67.4731]]]]\n",
"Food Region\n",
"[[[[164.621,-67.4318],[164.6342,-67.4359],[164.6393,-67.4412],[164.6375,-67.4493],[164.6266,-67.4542],[164.6124,-67.4566],[164.5942,-67.4542],[164.5834,-67.4509],[164.5771,-67.443],[164.581,-67.4382],[164.5874,-67.4343],[164.603,-67.4314],[164.612,-67.4314],[164.621,-67.4318]]]]\n",
"Food Region\n",
"[[[[164.5147,-67.5098],[164.4926,-67.496],[164.4881,-67.4878],[164.5011,-67.4582],[164.5013,-67.4515],[164.5834,-67.4509],[164.5942,-67.4542],[164.6183,-67.5099],[164.5147,-67.5098]]]]\n",
"Food Region\n",
"[[[[164.5999,-67.3461],[164.612,-67.4314],[164.6031,-67.4314],[164.5877,-67.4343],[164.5811,-67.4381],[164.5772,-67.4429],[164.5834,-67.4509],[164.5014,-67.4514],[164.5014,-67.4316],[164.492,-67.4153],[164.5387,-67.3712],[164.5784,-67.3504],[164.5999,-67.3461]]]]\n",
"Food Region\n",
"[[[[164.7151,-67.431],[164.7561,-67.4654],[164.7903,-67.5091],[164.7239,-67.5099],[164.6981,-67.4731],[164.6925,-67.4468],[164.7151,-67.431]]]]\n",
"Food Region\n",
"[[[[164.6982,-67.4731],[164.7238,-67.5099],[164.6184,-67.5099],[164.5943,-67.4543],[164.6125,-67.4567],[164.6265,-67.4543],[164.6376,-67.4493],[164.6982,-67.4731]]]]\n"
]
}
],
"source": [
"r = api.get('geoFeatures', params={'ou':'ou:USER_ORGUNIT_GRANDCHILDREN', 'displayProperty':'NAME'})\n",
"for i in r.json():\n",
" print(i['pn'])\n",
" print(i['co'])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.10"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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