malac-hd 0.1.1a1__tar.gz

malac-hd-0.1.1a1/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+  This version of the GNU Lesser General Public License incorporates
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malac-hd-0.1.1a1/MANIFEST.in

@@ -0,0 +1,3 @@
+graft malac
+global-exclude __pycache__
+global-exclude *.py[co]

malac-hd-0.1.1a1/PKG-INFO

@@ -0,0 +1,301 @@
+Metadata-Version: 2.1
+Name: malac-hd
+Version: 0.1.1a1
+Summary: Mapping Language Compiler for Health Data.
+Author-email: cdeHealth-Team <contact-project+cdehealth-malac-hd-52276676-issue-@incoming.gitlab.com>
+License:                    GNU LESSER GENERAL PUBLIC LICENSE
+                               Version 3, 29 June 2007
+        
+         Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+         Everyone is permitted to copy and distribute verbatim copies
+         of this license document, but changing it is not allowed.
+        
+        
+          This version of the GNU Lesser General Public License incorporates
+        the terms and conditions of version 3 of the GNU General Public
+        License, supplemented by the additional permissions listed below.
+        
+          0. Additional Definitions.
+        
+          As used herein, "this License" refers to version 3 of the GNU Lesser
+        General Public License, and the "GNU GPL" refers to version 3 of the GNU
+        General Public License.
+        
+          "The Library" refers to a covered work governed by this License,
+        other than an Application or a Combined Work as defined below.
+        
+          An "Application" is any work that makes use of an interface provided
+        by the Library, but which is not otherwise based on the Library.
+        Defining a subclass of a class defined by the Library is deemed a mode
+        of using an interface provided by the Library.
+        
+          A "Combined Work" is a work produced by combining or linking an
+        Application with the Library.  The particular version of the Library
+        with which the Combined Work was made is also called the "Linked
+        Version".
+        
+          The "Minimal Corresponding Source" for a Combined Work means the
+        Corresponding Source for the Combined Work, excluding any source code
+        for portions of the Combined Work that, considered in isolation, are
+        based on the Application, and not on the Linked Version.
+        
+          The "Corresponding Application Code" for a Combined Work means the
+        object code and/or source code for the Application, including any data
+        and utility programs needed for reproducing the Combined Work from the
+        Application, but excluding the System Libraries of the Combined Work.
+        
+          1. Exception to Section 3 of the GNU GPL.
+        
+          You may convey a covered work under sections 3 and 4 of this License
+        without being bound by section 3 of the GNU GPL.
+        
+          2. Conveying Modified Versions.
+        
+          If you modify a copy of the Library, and, in your modifications, a
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+        facility is invoked), then you may convey a copy of the modified
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+           ensure that, in the event an Application does not supply the
+           function or data, the facility still operates, and performs
+           whatever part of its purpose remains meaningful, or
+        
+           b) under the GNU GPL, with none of the additional permissions of
+           this License applicable to that copy.
+        
+          3. Object Code Incorporating Material from Library Header Files.
+        
+          The object code form of an Application may incorporate material from
+        a header file that is part of the Library.  You may convey such object
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+        material is not limited to numerical parameters, data structure
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+           for conveying Corresponding Source.)
+        
+          5. Combined Libraries.
+        
+          You may place library facilities that are a work based on the
+        Library side by side in a single library together with other library
+        facilities that are not Applications and are not covered by this
+        License, and convey such a combined library under terms of your
+        choice, if you do both of the following:
+        
+           a) Accompany the combined library with a copy of the same work based
+           on the Library, uncombined with any other library facilities,
+           conveyed under the terms of this License.
+        
+           b) Give prominent notice with the combined library that part of it
+           is a work based on the Library, and explaining where to find the
+           accompanying uncombined form of the same work.
+        
+          6. Revised Versions of the GNU Lesser General Public License.
+        
+          The Free Software Foundation may publish revised and/or new versions
+        of the GNU Lesser General Public License from time to time. Such new
+        versions will be similar in spirit to the present version, but may
+        differ in detail to address new problems or concerns.
+        
+          Each version is given a distinguishing version number. If the
+        Library as you received it specifies that a certain numbered version
+        of the GNU Lesser General Public License "or any later version"
+        applies to it, you have the option of following the terms and
+        conditions either of that published version or of any later version
+        published by the Free Software Foundation. If the Library as you
+        received it does not specify a version number of the GNU Lesser
+        General Public License, you may choose any version of the GNU Lesser
+        General Public License ever published by the Free Software Foundation.
+        
+          If the Library as you received it specifies that a proxy can decide
+        whether future versions of the GNU Lesser General Public License shall
+        apply, that proxy's public statement of acceptance of any version is
+        permanent authorization for you to choose that version for the
+        Library.
+        
+Project-URL: Homepage, https://gitlab.com/cdehealth/malac-hd
+Project-URL: Documentation, https://gitlab.com/cdehealth/malac-hd
+Project-URL: Release notes, https://gitlab.com/cdehealth/malac-hd/-/releases
+Project-URL: Source, https://gitlab.com/cdehealth/malac-hd
+Project-URL: Tracker, https://gitlab.com/cdehealth/malac-hd/-/issues
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: antlr4-python3-runtime>=4.13.0
+Requires-Dist: antlr4-tools>=0.2.1
+Requires-Dist: pytest>=7.0.0
+Requires-Dist: python-dateutil>=2.8.2
+Requires-Dist: lxml>=5.1.0
+
+# MaLaC-HD
+
+MaLaC-HD (MApping LAnguage Compiler for Health Data) is a tool that you can use to convert mappings between different health data formats to executable code. It can also be used as a library to dynamically execute mappings.
+
+## Why?
+
+When having parallel operations of some sort or another, there is one requirement that is challenging in the context of standardized APIs: mapping data, to make it accessible to the different worlds at least.
+
+There are many methods to map from one semi-structured data format to another. Most of the times, when a mapping requirement reveals, it is solved by a quick small script. After some time, that script needs technical or rule updates. As the rules are directly coded, they can only be altered by someone having knowledge about the mapping content, the mapping rules and the mapping technology. 
+
+To divide these concerns, HL7 FHIR created resources for mapping purposes, like the [StructureMap](https://www.hl7.org/fhir/structuremap.html) for [transformation](https://www.hl7.org/fhir/structuremap-operation-transform.html) and [ConceptMap](https://www.hl7.org/fhir/conceptmap.html) for [translation](https://www.hl7.org/fhir/conceptmap-operation-translate.html). Additionally a more human readable metalanguage for creating such StructureMap and ConceptMap resources was created, called [FHIR Mapping Language, or in short FML](https://www.hl7.org/fhir/mapping-language.html). Interestingly enough, FML is not restricted to FHIR as a source or target for the mapping. It could also be used i.e. to map from HL7 CDA to OHDSI OMOP CDM.
+
+Current FML or StructureMap/ConceptMap tools are quite slow in the transformation/translation of the content to be mapped, as both steps, the processing of the rules and the transformation/translation itself is done every time. As a gold standard and sparring partner for this project, the Canadian open source project [HAPI](https://github.com/hapifhir) with its Suisse extension [matchbox](https://www.matchbox.health/) has been used. Additionally, we got notice about some Italian project speeding up matchbox, but couldn't find any public references.
+
+We can't use current tools to map data synchronously, as nearly all mapping executions need more time than the [dorethy threshold of 0.4 seconds](https://lawsofux.com/doherty-threshold/), resulting in the users perception of "it got stuck". Also the practical, but restricted FHIR mapping language does not offer any possibilities to extend it with further functions, in contrast to the StructureMap and ConceptMap resources themselves, that could be easily extended.
+
+## How?
+
+Focusing on but not restricting to the health information technology world, a partnership was created out of the experts in the CDA2FHIR HL7 Austria Working Group, to solve this issue. On one side with expertise in research and on the other side with expertise in EHRs.
+
+By applying the MVP concept of build-measure-learn-repeat, first versions were created and tested against already existing FML-mappings in the HL7 community and matchbox as a mapping tool. 
+
+As the partners are themselves heavy users of the resulting MVPs, using them immediately after release, quick iterations of four months are planned.
+
+## What?
+
+MaLaC-HD is intended to focus on transformation speed and easy extensibility after compilation/convertion. This is achieved by seperation of 
+* the processing from FML to StructureMap/ConceptMap, 
+* the conversion from StructureMap/ConceptMap to python code, 
+* the execution of the translation itself from source to target. 
+It uses the mappings and requirements of some preliminary projects (i.e. https://github.com/HL7Austria/CDA2FHIR) as testing data.
+
+MaLaC-HD is not limited to the use of FML or StructureMap/ConceptMap for the translation, but has already implemented a conversion from StructureMap/ConceptMaps to python code. It can be used to transform/translate different input formats to different output formats, using some conversion/mapping rule language and the XSD or JSON schemas of the input and output format. It also makes it easier to develop new conversion or mapping rule languages, further input formats and/or extensions.
+
+## Pursued Objectives
+The development of MaLaC-HD focuses on the following three main objectives and their respective sub-objectives:
+
+- The compilation of the conversion/mapping rules by MaLaC-HD and the resulting mapping of these rules in a common programming language must be easily readable and directly related to the conversion/mapping rules.
+  - The conversion/mapping rules must be ballotable so that they can be queried and discussed for completeness and correctness as part of a guideline or even as a standalone part in a community, such as the HL7 community.
+- MaLaC-HD must not be dependent on any conversion rule language in order to be able to easily process conversion/mapping rules that can be mapped in different conversion rule languages.
+  - In particular, the limits of the respective conversion rule language require simple narrative extensibility in order to draw attention to the fact that further code must be added manually in the respective generated code by means of placeholders.
+- The result of compiling the conversion/mapping rules must be trimmed for speed and stability so as not to add any obstructive delays.
+  - The compiled conversion/mapping rules should be executable as stand-alone program code without MaLaC-HD.
+
+## Getting Started
+
+These instructions will get you a copy of the project up and running.
+
+### Installation
+
+Install malac-hd and its dependencies via pip:
+
+```
+pip install malac-hd
+```
+
+... or, if you want to build from source:
+
+
+```
+git clone https://gitlab.com/cdehealth/malac-hd.git
+cd malac-hd
+pip install -e .
+```
+
+#### Preparing your FML maps
+
+As the direct support of FML will come with the beta version this fall, a workaround has to be done right now in the alpha, by pre-compiling/converting the FML to StructreMaps and ConceptMaps by using the [java-validator](https://www.hl7.org/fhir/validator/), i.e.:
+```
+java -jar .\validator_cli.jar -ig ./tests/structuremap/aut_lab/cdaToBundle.map -output tests/structuremap/aut_lab/cda-2-bundle-merged-transform.4.fhir.xml -compile http://hl7.at/fhir/HL7ATCoreProfiles/4.0.1/StructureMap/at-cda-to-bundle -version 4.0
+```
+
+### Using MaLaC-HD
+
+with `malac-hd --help` you will get an overview:
+
+```
+____________________ MaLaC-HD 0.1.1+20240516-alpha started ____________________
+usage: malac-hd [-h] -m MAPPING [-co CONVERT_OUTPUT] [-ti TRANSFORM_INPUT] [-to TRANSFORM_OUTPUT] [-s]
+
+This is the MApping LAnguage Compiler for Health Data, short MaLaC-HD. We differentiate between two modes, converting and transforming. The convertion is compiling a given mapping to python code, that itself can be run with its own argument handling for transforming inputs. Additionally, the transformation can   
+also be be done by MaLaC-HD directly after convertion, i.e. for direct testing purposes.
+
+options:
+  -h, --help            show this help message and exit
+  -m MAPPING, --mapping MAPPING
+                        the mapping file path, the conversion/mapping rule language is detected by file ending, right now only StructureMaps and ConceptMaps can be given as mappings
+  -co CONVERT_OUTPUT, --convert_output CONVERT_OUTPUT
+                        the conversion python file path, if not given, saved in the working directory with the map-file name
+  -ti TRANSFORM_INPUT, --transform_input TRANSFORM_INPUT
+                        the transformation input file path, the ressource type is detected by its root node inside the xml
+  -to TRANSFORM_OUTPUT, --transform_output TRANSFORM_OUTPUT
+                        the transformation output file path, the ressource type is detected by its root node inside the xml
+  -s, --silent          do not print the converted python mapping to console
+```
+
+#### Example Usage 
+
+Usage of an in MaLaC-HD included example:
+```
+malac-hd -m ./tests/structuremap/aut_lab/cda-2-bundle-merged-transform.4.fhir.xml -co ./tests/structuremap/aut_lab/out/bundle.4.fhir.xml.py -i ./tests/structuremap/aut_lab/Lab_Allgemeiner_Laborbefund.at.cda.xml -to ./tests/structuremap/aut_lab/out/bundle.4.fhir.xml
+```
+
+## Support
+Please use our gitlab issues for questions or support.
+
+## Authors and acknowledgment
+We want to thank
+- [ELGA GmbH](https://www.elga.gv.at/) with their [CDA2FHIR](https://collab.hl7.at/display/BAL/AG+ELGA+CDA+Laborbefund+zu+FHIR) projects and
+- [AIT Austrian Institute of Technology GmbH](https://www.ait.ac.at/) with their [SmartFOX](https://www.smart-fox.at/) project.
+
+Additionally, we want to thank 
+- [Dave Kuhlman](https://davekuhlman.org/) with his open source implementation of [generateDS](https://www.davekuhlman.org/generateDS.html), making quick serializations of new data structures from their XSD schemas possible. 
+
+## License
+This is a LGPL licensed project, with a small add on that any usage of this project or results of this project should contain a for the consumer visible icon, that will be announced here in the near future.

malac-hd-0.1.1a1/README.md

@@ -0,0 +1,116 @@
+# MaLaC-HD
+
+MaLaC-HD (MApping LAnguage Compiler for Health Data) is a tool that you can use to convert mappings between different health data formats to executable code. It can also be used as a library to dynamically execute mappings.
+
+## Why?
+
+When having parallel operations of some sort or another, there is one requirement that is challenging in the context of standardized APIs: mapping data, to make it accessible to the different worlds at least.
+
+There are many methods to map from one semi-structured data format to another. Most of the times, when a mapping requirement reveals, it is solved by a quick small script. After some time, that script needs technical or rule updates. As the rules are directly coded, they can only be altered by someone having knowledge about the mapping content, the mapping rules and the mapping technology. 
+
+To divide these concerns, HL7 FHIR created resources for mapping purposes, like the [StructureMap](https://www.hl7.org/fhir/structuremap.html) for [transformation](https://www.hl7.org/fhir/structuremap-operation-transform.html) and [ConceptMap](https://www.hl7.org/fhir/conceptmap.html) for [translation](https://www.hl7.org/fhir/conceptmap-operation-translate.html). Additionally a more human readable metalanguage for creating such StructureMap and ConceptMap resources was created, called [FHIR Mapping Language, or in short FML](https://www.hl7.org/fhir/mapping-language.html). Interestingly enough, FML is not restricted to FHIR as a source or target for the mapping. It could also be used i.e. to map from HL7 CDA to OHDSI OMOP CDM.
+
+Current FML or StructureMap/ConceptMap tools are quite slow in the transformation/translation of the content to be mapped, as both steps, the processing of the rules and the transformation/translation itself is done every time. As a gold standard and sparring partner for this project, the Canadian open source project [HAPI](https://github.com/hapifhir) with its Suisse extension [matchbox](https://www.matchbox.health/) has been used. Additionally, we got notice about some Italian project speeding up matchbox, but couldn't find any public references.
+
+We can't use current tools to map data synchronously, as nearly all mapping executions need more time than the [dorethy threshold of 0.4 seconds](https://lawsofux.com/doherty-threshold/), resulting in the users perception of "it got stuck". Also the practical, but restricted FHIR mapping language does not offer any possibilities to extend it with further functions, in contrast to the StructureMap and ConceptMap resources themselves, that could be easily extended.
+
+## How?
+
+Focusing on but not restricting to the health information technology world, a partnership was created out of the experts in the CDA2FHIR HL7 Austria Working Group, to solve this issue. On one side with expertise in research and on the other side with expertise in EHRs.
+
+By applying the MVP concept of build-measure-learn-repeat, first versions were created and tested against already existing FML-mappings in the HL7 community and matchbox as a mapping tool. 
+
+As the partners are themselves heavy users of the resulting MVPs, using them immediately after release, quick iterations of four months are planned.
+
+## What?
+
+MaLaC-HD is intended to focus on transformation speed and easy extensibility after compilation/convertion. This is achieved by seperation of 
+* the processing from FML to StructureMap/ConceptMap, 
+* the conversion from StructureMap/ConceptMap to python code, 
+* the execution of the translation itself from source to target. 
+It uses the mappings and requirements of some preliminary projects (i.e. https://github.com/HL7Austria/CDA2FHIR) as testing data.
+
+MaLaC-HD is not limited to the use of FML or StructureMap/ConceptMap for the translation, but has already implemented a conversion from StructureMap/ConceptMaps to python code. It can be used to transform/translate different input formats to different output formats, using some conversion/mapping rule language and the XSD or JSON schemas of the input and output format. It also makes it easier to develop new conversion or mapping rule languages, further input formats and/or extensions.
+
+## Pursued Objectives
+The development of MaLaC-HD focuses on the following three main objectives and their respective sub-objectives:
+
+- The compilation of the conversion/mapping rules by MaLaC-HD and the resulting mapping of these rules in a common programming language must be easily readable and directly related to the conversion/mapping rules.
+  - The conversion/mapping rules must be ballotable so that they can be queried and discussed for completeness and correctness as part of a guideline or even as a standalone part in a community, such as the HL7 community.
+- MaLaC-HD must not be dependent on any conversion rule language in order to be able to easily process conversion/mapping rules that can be mapped in different conversion rule languages.
+  - In particular, the limits of the respective conversion rule language require simple narrative extensibility in order to draw attention to the fact that further code must be added manually in the respective generated code by means of placeholders.
+- The result of compiling the conversion/mapping rules must be trimmed for speed and stability so as not to add any obstructive delays.
+  - The compiled conversion/mapping rules should be executable as stand-alone program code without MaLaC-HD.
+
+## Getting Started
+
+These instructions will get you a copy of the project up and running.
+
+### Installation
+
+Install malac-hd and its dependencies via pip:
+
+```
+pip install malac-hd
+```
+
+... or, if you want to build from source:
+
+
+```
+git clone https://gitlab.com/cdehealth/malac-hd.git
+cd malac-hd
+pip install -e .
+```
+
+#### Preparing your FML maps
+
+As the direct support of FML will come with the beta version this fall, a workaround has to be done right now in the alpha, by pre-compiling/converting the FML to StructreMaps and ConceptMaps by using the [java-validator](https://www.hl7.org/fhir/validator/), i.e.:
+```
+java -jar .\validator_cli.jar -ig ./tests/structuremap/aut_lab/cdaToBundle.map -output tests/structuremap/aut_lab/cda-2-bundle-merged-transform.4.fhir.xml -compile http://hl7.at/fhir/HL7ATCoreProfiles/4.0.1/StructureMap/at-cda-to-bundle -version 4.0
+```
+
+### Using MaLaC-HD
+
+with `malac-hd --help` you will get an overview:
+
+```
+____________________ MaLaC-HD 0.1.1+20240516-alpha started ____________________
+usage: malac-hd [-h] -m MAPPING [-co CONVERT_OUTPUT] [-ti TRANSFORM_INPUT] [-to TRANSFORM_OUTPUT] [-s]
+
+This is the MApping LAnguage Compiler for Health Data, short MaLaC-HD. We differentiate between two modes, converting and transforming. The convertion is compiling a given mapping to python code, that itself can be run with its own argument handling for transforming inputs. Additionally, the transformation can   
+also be be done by MaLaC-HD directly after convertion, i.e. for direct testing purposes.
+
+options:
+  -h, --help            show this help message and exit
+  -m MAPPING, --mapping MAPPING
+                        the mapping file path, the conversion/mapping rule language is detected by file ending, right now only StructureMaps and ConceptMaps can be given as mappings
+  -co CONVERT_OUTPUT, --convert_output CONVERT_OUTPUT
+                        the conversion python file path, if not given, saved in the working directory with the map-file name
+  -ti TRANSFORM_INPUT, --transform_input TRANSFORM_INPUT
+                        the transformation input file path, the ressource type is detected by its root node inside the xml
+  -to TRANSFORM_OUTPUT, --transform_output TRANSFORM_OUTPUT
+                        the transformation output file path, the ressource type is detected by its root node inside the xml
+  -s, --silent          do not print the converted python mapping to console
+```
+
+#### Example Usage 
+
+Usage of an in MaLaC-HD included example:
+```
+malac-hd -m ./tests/structuremap/aut_lab/cda-2-bundle-merged-transform.4.fhir.xml -co ./tests/structuremap/aut_lab/out/bundle.4.fhir.xml.py -i ./tests/structuremap/aut_lab/Lab_Allgemeiner_Laborbefund.at.cda.xml -to ./tests/structuremap/aut_lab/out/bundle.4.fhir.xml
+```
+
+## Support
+Please use our gitlab issues for questions or support.
+
+## Authors and acknowledgment
+We want to thank
+- [ELGA GmbH](https://www.elga.gv.at/) with their [CDA2FHIR](https://collab.hl7.at/display/BAL/AG+ELGA+CDA+Laborbefund+zu+FHIR) projects and
+- [AIT Austrian Institute of Technology GmbH](https://www.ait.ac.at/) with their [SmartFOX](https://www.smart-fox.at/) project.
+
+Additionally, we want to thank 
+- [Dave Kuhlman](https://davekuhlman.org/) with his open source implementation of [generateDS](https://www.davekuhlman.org/generateDS.html), making quick serializations of new data structures from their XSD schemas possible. 
+
+## License
+This is a LGPL licensed project, with a small add on that any usage of this project or results of this project should contain a for the consumer visible icon, that will be announced here in the near future.

malac-hd-0.1.1a1/malac/hd/__init__.py

@@ -0,0 +1,33 @@
+from abc import ABC, abstractmethod
+
+__version__ = "0.1.1alpha1"
+
+class ConvertMaster(ABC):
+    @abstractmethod
+    def convert(self, input, o_module): # TODO:sbe adapt - this is not what is implemented/needed in base classes
+        pass
+        # return mapping_as_py
+
+# not sure if this class will be needed, it is only unsed inside the into py converted map
+
+
+class TransformMaster(ABC):
+    @abstractmethod
+    def transform(self, source_path, target_path):
+        pass
+
+list_m_modules = {  # this are modules that can be fully created for malac_hd or Subclasses extending modules that are fully generated by generateDS
+    # for StructureMapSub, in this module are additionally planned
+    # ConceptMapSub & StructureDefinitionSub (this one also uses
+    # ElementDefinitionSub with the <map> element)
+    ".4.fhir.xml": "fhir.r4.generator.resource",
+    #".4.fhir.map": "fhir4fml"
+}
+
+list_i_o_modules = { # this are modules that are fully generated by generateDS
+    "http://hl7.org/fhir/StructureDefinition":"fhir.r4",
+    "http://hl7.org/fhir/4.0/StructureDefinition":"fhir.r4",
+    #"http://hl7.org/fhir/StructureDefinition":"fhir5",
+    "http://hl7.org/fhir/cda/StructureDefinition":"cda.at_ext",
+    "http://hl7.org/cda/stds/core/StructureDefinition":"cda.at_ext"
+}