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IBMStreams#10: Contribute physionet adapter
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| # streamsx.health | ||
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| This community is focused on using Streams in the health care industry. Go to the wiki to participate in the discussion. | ||
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| https://github.com/IBMStreams/streamsx.health/wiki | ||
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ingest/physionet/com.ibm.streamsx.health.ingest.physionet/.classpath
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <classpath> | ||
| <classpathentry kind="src" output="impl/java/bin" path="impl/java/src"/> | ||
| <classpathentry exported="true" kind="con" path="com.ibm.streams.java/com.ibm.streams.operator"/> | ||
| <classpathentry exported="true" kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> | ||
| <classpathentry kind="src" path=".apt_generated"> | ||
| <attributes> | ||
| <attribute name="optional" value="true"/> | ||
| </attributes> | ||
| </classpathentry> | ||
| <classpathentry kind="output" path="impl/java/bin"/> | ||
| </classpath> |
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ingest/physionet/com.ibm.streamsx.health.ingest.physionet/.gitignore
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| /.apt_generated/ | ||
| /.toolkitList | ||
| /output/ | ||
| /toolkit.xml | ||
| /com.ibm.streamsx.health.physionet.PhysionetIngestService_temp.json |
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ingest/physionet/com.ibm.streamsx.health.ingest.physionet/.project
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>com.ibm.streamsx.health.ingest.physionet</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| <buildCommand> | ||
| <name>org.eclipse.jdt.core.javabuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.xtext.ui.shared.xtextBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>com.ibm.streams.studio.splproject.builder.SPLProjectBuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| </buildSpec> | ||
| <natures> | ||
| <nature>org.eclipse.xtext.ui.shared.xtextNature</nature> | ||
| <nature>com.ibm.streams.studio.splproject.SPLProjectNature</nature> | ||
| <nature>org.eclipse.jdt.core.javanature</nature> | ||
| </natures> | ||
| </projectDescription> |
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...health.ingest.physionet/.settings/application.PhysionetIngestService-BuildConfig.splbuild
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!DOCTYPE properties SYSTEM "http:https://java.sun.com/dtd/properties.dtd"> | ||
| <properties> | ||
| <comment>SPL Build Configuration: BuildConfig</comment> | ||
| <entry key="com.ibm.streams.studio.splproject:STATIC_LINKING">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:OPTIMIZED_CODE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:FUSION_MODE">FDEF</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:MAIN_COMPOSITE">application::PhysionetIngestService</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:NAME">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:GCC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:ACTIVE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:LD_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:PRE_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:DATA_DIR"/> | ||
| <entry key="com.ibm.streams.studio.splproject:POST_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:REPLACE_ENVIRONMENT">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:USE_PROJECT_DATA_DIR">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:PROFILING"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SDB">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:DEFAULT_POOL_SIZE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:OUTPUT_DIR">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:SAMPLING_RATE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:STANDALONE">F</entry> | ||
| </properties> |
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....ibm.streamsx.health.ingest.physionet.service.PhysionetIngestService-BuildConfig.splbuild
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| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!DOCTYPE properties SYSTEM "http:https://java.sun.com/dtd/properties.dtd"> | ||
| <properties> | ||
| <comment>SPL Build Configuration: BuildConfig</comment> | ||
| <entry key="com.ibm.streams.studio.splproject:STATIC_LINKING">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:OPTIMIZED_CODE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:FUSION_MODE">FDEF</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:MAIN_COMPOSITE">com.ibm.streamsx.health.ingest.physionet.service::PhysionetIngestService</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:NAME">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:GCC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:ACTIVE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:LD_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:PRE_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:DATA_DIR"/> | ||
| <entry key="com.ibm.streams.studio.splproject:POST_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:REPLACE_ENVIRONMENT">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:USE_PROJECT_DATA_DIR">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:PROFILING"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SDB">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:DEFAULT_POOL_SIZE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:OUTPUT_DIR">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:SAMPLING_RATE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:STANDALONE">F</entry> | ||
| </properties> |
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...bm.streamsx.health.ingest.physionet.service.test.PhysionetIngestTest-BuildConfig.splbuild
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!DOCTYPE properties SYSTEM "http:https://java.sun.com/dtd/properties.dtd"> | ||
| <properties> | ||
| <comment>SPL Build Configuration: BuildConfig</comment> | ||
| <entry key="com.ibm.streams.studio.splproject:STATIC_LINKING">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:OPTIMIZED_CODE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:FUSION_MODE">FDEF</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:MAIN_COMPOSITE">com.ibm.streamsx.health.ingest.physionet.service.test::PhysionetIngestTest</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:NAME">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:GCC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:ACTIVE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:LD_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:PRE_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:DATA_DIR"/> | ||
| <entry key="com.ibm.streams.studio.splproject:POST_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:REPLACE_ENVIRONMENT">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:USE_PROJECT_DATA_DIR">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:PROFILING"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SDB">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:DEFAULT_POOL_SIZE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:OUTPUT_DIR">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:SAMPLING_RATE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:STANDALONE">F</entry> | ||
| </properties> |
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...t/.settings/com.ibm.streamsx.health.physionet.PhysionetIngestService-BuildConfig.splbuild
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <!DOCTYPE properties SYSTEM "http:https://java.sun.com/dtd/properties.dtd"> | ||
| <properties> | ||
| <comment>SPL Build Configuration: BuildConfig</comment> | ||
| <entry key="com.ibm.streams.studio.splproject:STATIC_LINKING">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:OPTIMIZED_CODE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:FUSION_MODE">FDEF</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:MAIN_COMPOSITE">com.ibm.streamsx.health.physionet::PhysionetIngestService</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:NAME">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:GCC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SC_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:ACTIVE">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:LD_OPTS"/> | ||
| <entry key="com.ibm.streams.studio.splproject:PRE_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:DATA_DIR"/> | ||
| <entry key="com.ibm.streams.studio.splproject:POST_BUILD_CMD"/> | ||
| <entry key="com.ibm.streams.studio.splproject:REPLACE_ENVIRONMENT">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:USE_PROJECT_DATA_DIR">T</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:PROFILING"/> | ||
| <entry key="com.ibm.streams.studio.splproject:SDB">F</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:DEFAULT_POOL_SIZE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:OUTPUT_DIR">BuildConfig</entry> | ||
| <entry key="com.ibm.streams.studio.splproject:SAMPLING_RATE"/> | ||
| <entry key="com.ibm.streams.studio.splproject:STANDALONE">F</entry> | ||
| </properties> |
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...ysionet/com.ibm.streamsx.health.ingest.physionet/.settings/org.eclipse.core.runtime.prefs
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| eclipse.preferences.version=1 | ||
| line.separator=\n |
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...ysionet/com.ibm.streamsx.health.ingest.physionet/.settings/org.eclipse.jdt.apt.core.prefs
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| eclipse.preferences.version=1 | ||
| org.eclipse.jdt.apt.aptEnabled=true | ||
| org.eclipse.jdt.apt.reconcileEnabled=false |
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...t/physionet/com.ibm.streamsx.health.ingest.physionet/.settings/org.eclipse.jdt.core.prefs
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| eclipse.preferences.version=1 | ||
| org.eclipse.jdt.core.compiler.processAnnotations=enabled |
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ingest/physionet/com.ibm.streamsx.health.ingest.physionet/README.md
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| # Physionet Ingest Service | ||
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| Ingest data from physionet.org. To use this service, submit the following application: | ||
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| * com.ibm.streamsx.health.ingest.physionet.service::PhysionetIngestService | ||
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| This service requires the following submission parameter: | ||
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| * record.name - indicates what record to retrieve from Physionet. | ||
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| This service exports data with the following topic: | ||
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| * ingest-physionet | ||
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| Data is exported as JSON with the following schema: | ||
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| `type PublishJson_T = rstring jsonString;` | ||
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| To consume data in SPL, subscribe to the topic, the output schema of the susbribe operator should be PublishJson_T. | ||
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| To process data, convert JSON to the following SPL type: | ||
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| `type SignalECG_T = float64 ts, int32 ch1, int32 ch2 ; | ||
| type PatientECG_T = SignalECG_T, tuple<rstring patientId> ;` | ||
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| See com.ibm.streamsx.health.ingest.physionet.service.test::PhysionetIngestTest for details. |
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...t.physionet/com.ibm.streamsx.health.ingest.physionet.service.test/PhysionetIngestTest.spl
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| // begin_generated_IBM_copyright_prolog | ||
| // | ||
| // This is an automatically generated copyright prolog. | ||
| // After initializing, DO NOT MODIFY OR MOVE | ||
| //**************************************************************************** | ||
| // Copyright (C) 2016 International Business Machines Corporation | ||
| // All Rights Reserved | ||
| //**************************************************************************** | ||
| // end_generated_IBM_copyright_prolog | ||
| namespace com.ibm.streamsx.health.ingest.physionet.service.test ; | ||
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| use com.ibm.streamsx.health.ingest.physionet.service::* ; | ||
| use com.ibm.streamsx.topology.topic::Subscribe ; | ||
| use com.ibm.streamsx.json::JSONToTuple ; | ||
| use com.ibm.streamsx.health.ingest.physionet.service::PatientECG_T ; | ||
| use com.ibm.streamsx.inet.rest::HTTPTupleView ; | ||
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| use com.ibm.streamsx.health.ingest.types::*; | ||
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| composite PhysionetIngestTest | ||
| { | ||
| graph | ||
| (stream<PublishJson_T> Subscribe_1_out0) as Subscribe_1 = Subscribe() | ||
| { | ||
| param | ||
| topic : TOPIC() ; | ||
| streamType : PublishJson_T ; | ||
| } | ||
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| () as Custom_2 = Custom(JSONToTuple_3_out0 as inputStream) | ||
| { | ||
| logic | ||
| onTuple inputStream : | ||
| { | ||
| printStringLn((rstring) inputStream) ; | ||
| } | ||
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| } | ||
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| (stream<Observation_T> JSONToTuple_3_out0) as JSONToTuple_3 = | ||
| JSONToTuple(Subscribe_1_out0) | ||
| { | ||
| } | ||
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| () as ECGSignal = HTTPTupleView(JSONToTuple_3_out0 as inPort0Alias) | ||
| { | ||
| window | ||
| inPort0Alias : sliding, count(1000), time(1.0) ; | ||
| param | ||
| port: 8080; | ||
| } | ||
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| } | ||
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