Merge pull request #5 from grongierisc/master

Add python experience on datapipe flows

Author: isc-afuentes

.gitignore

@@ -1,2 +1,15 @@
 *.log
-data/input/*.hl7
+data/input/*.hl7
+data/output/
+# Python stuff:
+*.pyc
+*.pyo
+# virtualenv
+.venv
+# dist
+dist
+# build
+build
+# eggs
+*.egg
+*.egg-info

Dockerfile

@@ -1,4 +1,4 @@
-ARG IMAGE=intersystemsdc/irishealth-community:2022.2.0.368.0-zpm
+ARG IMAGE=intersystemsdc/irishealth-community:latest
 FROM $IMAGE
 
 USER root
@@ -24,7 +24,17 @@ COPY --chown=irisowner:irisowner src src
 COPY --chown=irisowner:irisowner module.xml module.xml
 COPY --chown=irisowner:irisowner Installer.cls Installer.cls
 
+ENV PATH "/home/irisowner/.local/bin:/usr/irissys/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/irisowner/bin"
+
+RUN pip install iris-pex-embedded-python
+
+## Python stuff
+ENV IRISUSERNAME "SuperUser"
+ENV IRISPASSWORD "SYS"
+ENV IRISNAMESPACE "DPIPE"
+
 # run iris.script
 RUN iris start IRIS \
     && iris session IRIS < /opt/irisapp/iris.script \
+    && iop -m /opt/irisapp/src/python/Demo/settings.py \
     && iris stop IRIS quietly

README.md

@@ -11,6 +11,10 @@ docker compose up -d
 
 * Log-in to the system using `superuser` / `SYS`.
 
+* Start an inteoperability production in *Interoperability > List > Productions*:
+  * `DataPipe.Test.Production` - regular objectscript DataPipe demo production
+  * `DataPipe.Python.Production` - Python implemented DataPiepe demo production
+
 * Generate sample data using [WebTerminal](http://localhost:52773/terminal/)
 ```objectscript
 do ##class(DataPipe.Test.HL7.Helper).GenerateFilesHL7ADT(100)

docker-compose.yml

@@ -9,8 +9,8 @@ services:
     container_name: datapipe
     init: true
     ports:
-    - "1972:1972"
-    - "52773:52773"
+    - 1972:1972
+    - 52773:52773
     volumes:
     - .:/app
     networks:

iris.script

@@ -3,6 +3,12 @@
     set $namespace = "%SYS"
     do ##class(Security.Users).UnExpireUserPasswords("*")
 
+    //Service for embedded python
+    do ##class(Security.Services).Get("%Service_CallIn",.prop)
+    set prop("Enabled")=1
+    set prop("AutheEnabled")=48
+    do ##class(Security.Services).Modify("%Service_CallIn",.prop)
+
     // create ns for dev environment
     do $SYSTEM.OBJ.Load("/opt/irisapp/Installer.cls", "ck") 
 
@@ -24,6 +30,5 @@
     // auto start interop production
     set production = "DataPipe.Test.Production"
     set ^Ens.Configuration("csp","LastProduction") = production
-    do ##class(Ens.Director).SetAutoStart(production)
 
     halt

module.xml

@@ -3,7 +3,7 @@
   <Document name="iris-datapipe.ZPM">
     <Module>
       <Name>iris-datapipe</Name>
-      <Version>0.0.1</Version>
+      <Version>0.0.2</Version>
       <Description>DataPipe an interoperability framework to ingest data in InterSystems IRIS in a flexible way.</Description>
       <Keywords>datapipe ingestion staging validation</Keywords>
       <Author>
@@ -19,6 +19,13 @@
           <Version>>=1.0.8</Version>
         </ModuleReference>
       </Dependencies>
+      <Dependencies>
+        <ModuleReference>
+          <Name>pex-embbeded-python</Name>
+          <Version>>=2.0.0</Version>
+        </ModuleReference>
+      </Dependencies>
+      <FileCopy Name="src/python/DataPipe" Target="${libdir}python/DataPipe/"/>
       <SourcesRoot>src</SourcesRoot>
       <Resource Name="DataPipe.PKG"/>
       <CSPApplication 

pyproject.toml

@@ -0,0 +1,59 @@
+# Licensed under the MIT License
+# https://github.com/grongierisc/iris_datapipe/blob/main/LICENSE
+
+import os
+
+from setuptools import setup
+
+def package_files(directory):
+    paths = []
+    for (path, directories, filenames) in os.walk(directory):
+        for filename in filenames:
+            paths.append(os.path.join('.', path, filename))
+    return paths
+
+extra_files = package_files('src/python/')
+
+def main():
+    # Read the readme for use as the long description
+    with open(os.path.join(os.path.abspath(os.path.dirname(__file__)),
+                            'README.md'), encoding='utf-8') as readme_file:
+        long_description = readme_file.read()
+
+    # Do the setup
+    setup(
+        name='iris_datapipe',
+        description='iris_datapipe',
+        long_description=long_description,
+        long_description_content_type='text/markdown',
+        version='0.0.2',
+        author='grongier',
+        author_email='guillaume.rongier@intersystems.com',
+        keywords='iris_datapipe',
+        url='https://github.com/grongierisc/iris-datapipe',
+        license='MIT',
+        classifiers=[
+            'Development Status :: 5 - Production/Stable',
+            'Intended Audience :: Developers',
+            'License :: OSI Approved :: MIT License',
+            'Operating System :: OS Independent',
+            'Programming Language :: Python :: 3.6',
+            'Programming Language :: Python :: 3.7',
+            'Programming Language :: Python :: 3.8',
+            'Programming Language :: Python :: 3.9',
+            'Programming Language :: Python :: 3.10',
+            'Programming Language :: Python :: 3.11',
+            'Topic :: Utilities'
+        ],
+        package_dir={'': 'src/python'},
+        packages=['DataPipe'],
+
+        python_requires='>=3.6',
+        install_requires=[
+            "iris-pex-embedded-python>=2.0.0"
+        ]
+    )
+
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -88,7 +88,9 @@ ClassMethod queryFIND() As %String
 
 /// Get an Inbox record, querying by key attributes
 /// This method is used to determine if an Inbox record can be re-used
-ClassMethod GetByKeyAttributes(att As InboxAttributes, Output obj As Inbox) As %Status
+ClassMethod GetByKeyAttributes(
+	att As InboxAttributes,
+	Output obj As Inbox) As %Status
 {
 	set ret = $$$OK
 	try {
@@ -115,7 +117,10 @@ ClassMethod GetByKeyAttributes(att As InboxAttributes, Output obj As Inbox) As %
 
 /// Calculate a SQL field given an Inbox ID
 /// This method is used by calculated SQL fields
-ClassMethod CalcSqlFieldById(field As %String, default As %String, id As %String) As %String
+ClassMethod CalcSqlFieldById(
+	field As %String,
+	default As %String,
+	id As %String) As %String
 {
 	set ret = default
 	try {

src/DataPipe/Data/Inbox.cls

@@ -12,8 +12,17 @@ Parameter FORMORDERBY As %String = "Id";
 /// *Calculated* Id. %ID value projected to JSON
 Property Id As %Integer(%JSONINCLUDE = "OUTPUTONLY") [ Calculated, SqlComputeCode = { set {*}={%%ID}}, SqlComputed ];
 
+/// Model Is Python
+Property ModelIsPython As %Boolean(%JSONINCLUDE = "NONE") [ InitialExpression = 0 ];
+
+/// Model class name
+Property ModelModule As %String(%JSONINCLUDE = "NONE", MAXLEN = "");
+
+/// Model Module path
+Property ModelClassPath As %String(%JSONINCLUDE = "NONE", MAXLEN = "");
+
 /// Model class name 
-Property ModelName As %String(MAXLEN="");
+Property ModelName As %String(MAXLEN = "");
 
 /// Model serialized data
 Property ModelData As %Stream.GlobalCharacter;
@@ -81,6 +90,15 @@ Storage Default
 <Value name="12">
 <Value>HeaderId</Value>
 </Value>
+<Value name="13">
+<Value>ModelIsPython</Value>
+</Value>
+<Value name="14">
+<Value>ModelModule</Value>
+</Value>
+<Value name="15">
+<Value>ModelClassPath</Value>
+</Value>
 </Data>
 <DataLocation>^DataPipe.Data.IngestionD</DataLocation>
 <DefaultData>IngestionDefaultData</DefaultData>

src/DataPipe/Data/Ingestion.cls

@@ -57,8 +57,9 @@ Method SerializeValidationErrors() As %Status
 	try {
     set count = ..ValidationErrors.Count()
 	for i=1:1:count {
-      set code = ..ValidationErrors.GetAt(i).Code
-      set desc = ..ValidationErrors.GetAt(i).Desc
+	  set err = ..ValidationErrors.GetAt(i)
+      set code = err.Code
+      set desc = err.Desc
       set jsonError = code_": "_desc
       do jsonArr.%Push(jsonError)
 	}

src/DataPipe/Data/Staging.cls

@@ -0,0 +1,21 @@
+Class DataPipe.Helper Extends %RegisteredObject
+{
+
+ClassMethod SetPythonPath(pClasspaths)
+{
+    set sys = ##class(%SYS.Python).Import("sys")
+    do sys.path.append(pClasspaths)
+}
+
+ClassMethod GetPythonInstance(
+	pModule,
+	pRemoteClassname) As %SYS.Python
+{
+    set importlib = ##class(%SYS.Python).Import("importlib")
+    set builtins = ##class(%SYS.Python).Import("builtins")
+    set module = importlib."import_module"(pModule)
+    set class = builtins.getattr(module, pRemoteClassname)
+    return class."__new__"(class)
+}
+
+}

src/DataPipe/Helper.cls

@@ -6,7 +6,9 @@ Method Serialize(Output stream) As %Status
     Quit $$$ERROR($$$NotImplemented)
 }
 
-ClassMethod Deserialize(stream As %Stream.Object, Output obj) As %Status
+ClassMethod Deserialize(
+	stream As %Stream.Object,
+	Output obj) As %Status
 {
     Quit $$$ERROR($$$NotImplemented)
 }
@@ -26,7 +28,10 @@ Method GetOperation() As %Status
     Quit $$$ERROR($$$NotImplemented)
 }
 
-Method RunOperation(Output errorList As %List, Output log As %Stream.Object, bOperation As Ens.BusinessOperation = "") As %Status
+Method RunOperation(
+	Output errorList As %List,
+	Output log As %Stream.Object,
+	bOperation As Ens.BusinessOperation = "") As %Status
 {
     Quit $$$ERROR($$$NotImplemented)
 }

src/DataPipe/Model.cls

@@ -5,7 +5,9 @@ Parameter ADAPTER;
 
 Parameter INVOCATION = "Queue";
 
-Method OperationHandler(pRequest As DataPipe.Msg.OperReq, Output pResponse As Ens.Response) As %Status
+Method OperationHandler(
+	pRequest As DataPipe.Msg.OperReq,
+	Output pResponse As Ens.Response) As %Status
 {
 	set ret = $$$OK
 	try {
@@ -19,10 +21,20 @@ Method OperationHandler(pRequest As DataPipe.Msg.OperReq, Output pResponse As En
 		$$$ThrowOnError(operObj.%Save())
 
 		// deserialize model
-		set modelData = pRequest.data.ModelNormData
-        set modelName = pRequest.data.Ingestion.ModelName
-        set sc = $classmethod(modelName, "Deserialize", modelData, .modelObj)
-        $$$ThrowOnError(sc)
+        if pRequest.data.Ingestion.ModelIsPython {
+            // Set python path
+            do ##class(DataPipe.Helper).SetPythonPath(pRequest.data.Ingestion.ModelClassPath)
+            set modelObj = ##class(DataPipe.Helper).GetPythonInstance(pRequest.data.Ingestion.ModelModule, pRequest.data.Ingestion.ModelName)
+            do modelObj.Deserialize(pRequest.data.ModelNormData)
+			set errorList = ""
+			set operLog = ""
+
+        } else {
+			set modelData = pRequest.data.ModelNormData
+			set modelName = pRequest.data.Ingestion.ModelName
+			set sc = $classmethod(modelName, "Deserialize", modelData, .modelObj)
+			$$$ThrowOnError(sc)
+		}
 
 		set operLog = ""
 		set operationSC = $$$OK
@@ -34,15 +46,37 @@ Method OperationHandler(pRequest As DataPipe.Msg.OperReq, Output pResponse As En
 
 		// not ignored - perfom operation	
 		} else {
-			set operationSC = modelObj.RunOperation(.errorList, .operLog, ##this)
+			if pRequest.data.Ingestion.ModelIsPython {
+				// Python doesn't support byref parameters, so we return error list and oper log as strings
+				try {
+					set operationSC = $$$OK
+					set pythonList = modelObj.RunOperation(##this)
+					set errorList = ##class(%ListOfDataTypes).%New()
+					set operLog = ##class(%Stream.GlobalCharacter).%New()
+                	for i=1:1:pythonList.Count() {
+						set err = pythonList.GetAt(i)
+						if err.Code = "OPERATION"
+						{   
+							set operationSC = $$$ERROR($$$GeneralError, err.Desc)
+						} if err.Code = "OPERLOG" {
+							do operLog.WriteLine(err.Desc)
+						} else {
+							do errorList.Insert(err)
+						}
+                	}
+				} catch ex {
+					set operationSC = ex.AsStatus()
+				}
+			} else {
+				set operationSC = modelObj.RunOperation(.errorList, .operLog, ##this)
+			}
 			set operObj.Retries = operObj.Retries + 1
 			if $$$ISOK(operationSC) {
 				set operObj.Status = "PROCESSED"
 				set inboxObj.Status = "DONE"
 			} else {
 				set operObj.Status = "ERROR"
 				set inboxObj.Status = "ERROR-OPERATING"
-
 				// serialize errors
 				set operObj.OperErrors = errorList
 				$$$ThrowOnError(operObj.SerializeOperErrors())

src/DataPipe/Oper/BO/OperationHandler.cls

@@ -41,11 +41,19 @@ Method DeserializeModel() As %Status
 {
     set ret = $$$OK
     try {
-        set modelData = ..Oper.Staging.ModelNormData
-        set modelName = ..Oper.Staging.Ingestion.ModelName
-        set sc = $classmethod(modelName, "Deserialize", modelData, .obj)
-        $$$ThrowOnError(sc)
-        set ..Model = obj
+        if ..Oper.Staging.Ingestion.ModelIsPython {
+            // Set python path
+            do ##class(DataPipe.Helper).SetPythonPath(..Oper.Staging.Ingestion.ModelClassPath)
+            set ..Model = ##class(DataPipe.Helper).GetPythonInstance(..Oper.Staging.Ingestion.ModelModule, ..Oper.Staging.Ingestion.ModelName)
+            do ..Model.Deserialize(..Oper.Staging.ModelNormData)
+
+        } else {
+            set modelData = ..Oper.Staging.ModelNormData
+            set modelName = ..Oper.Staging.Ingestion.ModelName
+            set sc = $classmethod(modelName, "Deserialize", modelData, .obj)
+            $$$ThrowOnError(sc)
+            set ..Model = obj
+        }
 
     } catch ex {
         set ret = ex.AsStatus()

src/DataPipe/Oper/BP/OperManagerContext.cls

@@ -6,7 +6,9 @@ Property TargetConfigName As %String;
 
 Parameter SETTINGS = "TargetConfigName:Basic:selector?context={Ens.ContextSearch/ProductionItems?targets=1&productionName=@productionId}";
 
-ClassMethod OnGetConnections(ByRef pArray As %String, pItem As Ens.Config.Item)
+ClassMethod OnGetConnections(
+	ByRef pArray As %String,
+	pItem As Ens.Config.Item)
 {
   Do pItem.PopulateModifiedSettings()
 	Set (tValue,tIndex)="" For {