malac-hd 0.1.1a1__py3-none-any.whl

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"
+}

malac/hd/__main__.py

@@ -0,0 +1,98 @@
+import argparse
+import os
+import time
+import sys
+import importlib.util
+# dynamic import by init_class()!
+
+if __package__ != "malac.hd":
+    current = os.path.dirname(os.path.realpath(__file__))
+    parent = os.path.dirname(current)
+    sys.path.append(parent)
+import malac.hd
+
+
+description_text = """You are using the MApping LAnguage Compiler for Health Data, short MaLaC-HD.
+We differentiate between two modes, CONVERTING and TRANSFORMING.
+The CONVERTION is done by compiling a given mapping to python code, that itself can be run with its own argument handling for TRANSFORMING input files.
+Additionally, the TRANSFORMATION can also be be done by MaLaC-HD directly after CONVERTION, i.e. for direct testing purposes."""
+auto_detect = "the ressource type is detected by its root node inside the xml"
+
+
+def init_argparse(script) -> argparse.ArgumentParser:
+    if script:
+        prog = "malac-hd"
+    else:
+        prog = "python -m malac.hd"
+    parser = argparse.ArgumentParser(prog=prog, description=description_text, formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument(
+        "-m", "--mapping", help='the mapping file path, the conversion/mapping rule language is detected by file ending, right now only FHIR R4 (*.4.fhir.xml) StructureMaps and ConceptMaps can be given as mappings', required=True
+    )
+    parser.add_argument(
+        "-co", "--convert_output", help='the conversion python file path, if not given, saved in the working directory with the map-file name', required=False
+    )
+    
+    parser.add_argument(
+        "-ti", "--transform_input", help='the transformation input file path, '+auto_detect, required=False
+    )
+    parser.add_argument(
+        "-to", "--transform_output", help='the transformation output file path, '+auto_detect, required=False
+    )
+    
+    parser.add_argument(
+        "-s", "--silent", action="store_true", help='do not print the converted python mapping to console', required=False
+    )
+    return parser
+
+
+def get_standard_by_fileending(filename, list_classes, return_ending_not_class=False):
+    for iclass in list_classes:
+        if filename.endswith(iclass):
+            if return_ending_not_class:
+                return iclass
+            return list_classes[iclass]
+    sys.exit("The classification could not be detected from the file name. \n %s" % description_text)
+
+
+def main(script) -> None:
+    start = time.time()
+    print("____________________ MaLaC-HD "+malac.hd.__version__+" started ____________________")
+
+    parser = init_argparse(script)
+    args = parser.parse_args()
+
+    print("Converting "+args.mapping)
+
+    module_name = get_standard_by_fileending(args.mapping, malac.hd.list_m_modules)
+    module_split = ["malac", "hd", "compiler"] + module_name.split(".")
+    m_module = getattr(__import__(".".join(module_split[:-1]), fromlist=[module_split[-1]]), module_split[-1])
+    map = m_module.parse(args.mapping, silence=True)
+
+    py_code = map.convert(silent=args.silent, source=os.path.abspath(args.mapping))
+
+    # as similar as possible to https://www.hl7.org/fhir/resource-operation-convert.html
+    if args.convert_output:
+        if os.path.isfile(args.convert_output):
+            os.remove(args.convert_output)
+        with open(args.convert_output, 'w', newline='', encoding='utf-8') as f:
+            f.write(py_code)
+
+    # as similar as possible to https://www.hl7.org/fhir/structuremap-operation-transform.html
+    # if args.output is full file path, then do the transform itself we just created
+    if args.transform_output and args.transform_input:
+        print("")
+        spec = importlib.util.spec_from_loader("mapping", loader=None)
+        module = importlib.util.module_from_spec(spec)
+        exec(py_code, module.__dict__)
+        module.transform(args.transform_input, args.transform_output)
+        print("")
+
+    print("altogether in "+str(round(time.time()-start,3))+" seconds.")
+    print("____________________ MaLaC-HD "+malac.hd.__version__+" ended ____________________")
+
+
+def script_main():
+    main(script=True)
+
+if __name__ == '__main__':
+    main(script=False)

malac/hd/compiler/fhir/r4/generator/__init__.py

@@ -0,0 +1,4 @@
+from .resource import *
+from .structuremap import *
+from .conceptmap import *
+from .structuredefinition import *

malac/hd/compiler/fhir/r4/generator/conceptmap.py

@@ -0,0 +1,348 @@
+
+import sys
+import json
+
+import malac.hd
+from malac.models.fhir import r4 as supermod
+
+class PythonGenerator(supermod.ConceptMap, malac.hd.ConvertMaster):
+    from collections import defaultdict
+    con_map_6d = None
+
+    def __init__(self, id=None, meta=None, implicitRules=None, language=None, text=None, contained=None, extension=None, modifierExtension=None, url=None, identifier=None, version=None, name=None, title=None, status=None, experimental=None, date=None, publisher=None, contact=None, description=None, useContext=None, jurisdiction=None, purpose=None, copyright=None, sourceUri=None, sourceCanonical=None, targetUri=None, targetCanonical=None, group=None, **kwargs_):
+        super(PythonGenerator, self).__init__(id, meta, implicitRules, language, text, contained, extension, modifierExtension, url, identifier, version, name, title, status, experimental, date, publisher, contact, description, useContext, jurisdiction, purpose, copyright, sourceUri, sourceCanonical, targetUri, targetCanonical, group,  **kwargs_)
+
+    # the source param is not beeing handled, because there are no known possbilities of importing/including conceptMaps in other conceptMaps
+    def convert(self, silent=True, return_header_and_footer_for_standalone=True, source=".", return_translate_def=True, return_dict_add=True):  # TODO:sbe replace source and return_XXX with context/params, to make more generic
+        self.py_code = ""
+        if return_header_and_footer_for_standalone:
+            self._header_standalone()
+        if return_translate_def:
+            self._header_translate_def()
+        if return_dict_add:
+            self.con_map_6d = self.nested_dict(5, list)
+            for one_group in self.get_group():
+                for one_element in one_group.get_element():
+                    for one_target in one_element.get_target():
+                        self.con_map_6d \
+                            [tmp.get_value() if (tmp := self.get_sourceUri()) or (tmp := self.get_sourceCanonical()) else "%"] \
+                            [tmp.get_value() if (tmp := self.get_targetUri()) or (tmp := self.get_targetCanonical()) else "%"] \
+                            [tmp.get_value() if (tmp := one_group.get_source()) else "%"] \
+                            [tmp.get_value() if (tmp := one_group.get_target()) else "%"] \
+                            [tmp.get_value() if (tmp := one_element.get_code()) else "%"] \
+                            .append({"equivalence":one_target.get_equivalence().get_value(), 
+                                    "concept":{
+                                        "system": tmp.get_value() if (tmp := one_group.get_source()) else "", 
+                                        "version": "", # TODO version of codesystem out of url?
+                                        "code": tmp.get_value() if (tmp := one_target.get_code()) else "",
+                                        "display": tmp.get_value() if (tmp := one_target.get_display()) else "",
+                                        "userSelected": False},
+                                    "source": tmp.get_value() if (tmp := self.get_url()) or (tmp := self.get_id()) else "%"})
+                
+                if unmapped := one_group.get_unmapped(): # using as many unsafe url characters here, that really should not be used as system id/url or codes of a real codesystem, like [ ] { } | \ ” % ~ # < >
+                    tmp_equivalence = "inexact"
+                    tmp_code = ""
+                    tmp_display = ""
+                    tmp_code_lvl = ""
+                    if unmapped.get_mode().get_value() == "provided":
+                        tmp_code_lvl = "|"
+                        tmp_equivalence = "equal"
+                        tmp_code = "|" + (tmp.get_value() if (tmp := unmapped.get_code()) else "") 
+                    elif unmapped.get_mode().get_value() == "fixed":
+                        tmp_code_lvl = "~"
+                        tmp_code = "~"+unmapped.get_code().get_value() # must be given if fixed
+                        tmp_display = unmapped.get_display().get_value() or ""
+                    elif unmapped.get_mode().get_value() == "other-map":
+                        #tmp_match = "lambda: translate(url="+unmapped.get_url()+", conceptMapVersion=conceptMapVersion, code=code, system=system, version=version, source=source, coding=coding, codeableConcept=codeableConcept, target=target, targetsystem=targetsystem, reverse=reverse, silent=silent)" # cant access the varibales inside the dict...
+                        tmp_code_lvl = "#"
+                        tmp_code = "#"+unmapped.get_url().get_value()
+                    else:
+                        sys.exit(unmapped.get_mode()+" as mode for unmapped is not defined! Please use the modes from https://hl7.org/fhir/R4B/valueset-conceptmap-unmapped-mode.html .")
+                    self.con_map_6d \
+                        [tmp.get_value() if (tmp := self.get_sourceUri()) or (tmp := self.get_sourceCanonical()) else "%"] \
+                        [tmp.get_value() if (tmp := self.get_targetUri()) or (tmp := self.get_targetCanonical()) else "%"] \
+                        [tmp.get_value() if (tmp := one_group.get_source()) else "%"] \
+                        [tmp.get_value() if (tmp := one_group.get_target()) else "%"] \
+                        [tmp_code_lvl] \
+                        .append({"equivalence":tmp_equivalence, 
+                                "concept":{
+                                    "system": "", 
+                                    "version": "", # TODO version of codesystem out of url?
+                                    "code": tmp_code,
+                                    "display": tmp_display,
+                                    "userSelected": False},
+                                "source": tmp.get_value() if (tmp := self.get_url()) or (tmp := self.get_id()) else "%"})
+
+            self.py_code += "\n"
+            j_dump = json.dumps(self.con_map_6d, indent=4)
+            # replace all the json lower case bools to python usual pascal case bools
+            j_dump = j_dump.replace(": false",": False").replace(": true",": True")
+            self.py_code += 'con_map_7d["'+(tmp.get_value() if (tmp := self.get_url()) or (tmp := self.get_id()) else "%")+'"] = ' + j_dump
+            
+        if return_header_and_footer_for_standalone:
+            self._footer_standalone()
+
+        if not silent:
+            print("\n%s" % self.py_code)
+        
+        return self.py_code
+        
+    # from https://stackoverflow.com/a/39819609/6012216
+    def nested_dict(self, n, type): 
+        if n == 1:
+            return self.defaultdict(type)
+        else:
+            return self.defaultdict(lambda: self.nested_dict(n-1, type))  
+
+    def _header_standalone(self):
+        self.py_code += '''import argparse
+import time
+import malac.models.fhir.r4 as fhir4
+import sys
+
+description_text = "This has been compiled by the MApping LAnguage Compiler for Health Data, short MaLaC-HD. See arguments for more details."
+
+def init_argparse() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description=description_text)
+    parser.add_argument(
+       '-c', '--code', help="""code --	
+The code that is to be translated. If a code is provided, a system must be provided""",
+        required=True
+    )
+    parser.add_argument(
+       '-sys', '--system', help="""uri --	
+The system for the code that is to be translated""",
+        required=True
+    )
+    parser.add_argument(
+       '-ver', '--version', help="""string --	
+The version of the system, if one was provided in the source data""",
+        required=True
+    )
+    parser.add_argument(
+       '-s', '--source', help="""uri --	
+Identifies the value set used when the concept (system/code pair) was chosen. 
+May be a logical id, or an absolute or relative location. 
+The source value set is an optional parameter because in some cases, the client cannot know what the source value set is. 
+However, without a source value set, the server may be unable to safely identify an applicable concept map, 
+and would return an error. For this reason, a source value set SHOULD always be provided. 
+Note that servers may be able to identify an appropriate concept map without a source value set 
+if there is a full mapping for the entire code system in the concept map, or by manual intervention""",
+        required=True
+    )
+    parser.add_argument(
+       '-cg', '--coding', help="""Coding --	
+A coding to translate""",
+        required=True
+    )
+    parser.add_argument(
+       '-cc', '--codeableConcept', help="""CodeableConcept --	
+A full codeableConcept to validate. The server can translate any of the coding values (e.g. existing translations) 
+as it chooses""",
+        required=True
+    )
+    parser.add_argument(
+       '-t', '--target', help="""uri -- 
+Identifies the value set in which a translation is sought. May be a logical id, or an absolute or relative location. 
+If there's no target specified, the server should return all known translations, along with their source""", 
+        required=True
+    )
+    parser.add_argument(
+       '-ts', '--targetsystem', help="""uri -- 
+Identifies a target code system in which a mapping is sought. This parameter is an alternative to the target parameter - 
+only one is required. Searching for any translation to a target code system irrespective of the context (e.g. target valueset) 
+may lead to unsafe results, and it is at the discretion of the server to decide when to support this operation""", 
+        required=True
+    )
+    parser.add_argument(
+       '-r', '--reverse', action="store_true", help="""boolean -- True if stated, else False -- 
+If this is true, then the operation should return all the codes that might be mapped to this code. 
+This parameter reverses the meaning of the source and target parameters""", 
+        required=True
+    )
+    parser.add_argument(
+       '-st', '--silent', action="store_true", help="""boolean -- True if stated, else False --
+Do not print the converted python mapping to console""", 
+        required=True
+    )
+    return parser
+'''
+
+    def _header_translate_def(self): 
+        self.py_code += '''
+# output
+# 1..1 result (boolean)
+# 0..1 message with error details for human (string)
+# 0..* match with (list)
+#   0..1 equivalnce (string from https://hl7.org/fhir/R4B/valueset-concept-map-equivalence.html)
+#   0..1 concept
+#       0..1 system
+#       0..1 version
+#       0..1 code
+#       0..1 display 
+#       0..1 userSelected will always be false, because this is a translation
+#   0..1 source (conceptMap url)
+# TODO implement reverse
+def translate(url=None, conceptMapVersion=None, code=None, system=None, version=None, source=None, coding=None, codeableConcept=None, target=None, targetsystem=None, reverse=None, silent=False)\
+              -> dict [bool, str, list[dict[str, dict[str, str, str, str, bool], str]]]:
+    start = time.time()
+    
+    # start validation and recall of translate in simple from
+    if codeableConcept:
+        if isinstance(codeableConcept, str): 
+            codeableConcept = fhir4.parseString(codeableConcept, silent)
+        elif isinstance(coding, fhir4.CodeableConcept):
+            pass
+        else:
+            sys.exit("The codeableConcept parameter has to be a string or a CodeableConcept Object (called method as library)!")
+        # the first fit will be returned, else the last unfitted value will be returned
+        # TODO check translate params
+        for one_coding in codeableConcept.get_coding:
+            if (ret := translate(url=url, source=source, coding=one_coding, 
+                                 target=target, targetsystem=targetsystem, 
+                                 reverse=reverse, silent=True))[0]:
+                return ret
+        else: return ret
+        
+    elif coding:
+        if isinstance(coding, str): 
+            coding = fhir4.parseString(coding, silent)
+        elif isinstance(coding, fhir4.Coding):
+            pass
+        else:
+            sys.exit("The coding parameter has to be a string or a Coding Object (called method as library)!")
+        # TODO check translate params
+        return translate(url=url,  source=source, coding=one_coding, 
+                         target=target, targetsystem=targetsystem, 
+                         reverse=reverse, silent=True)
+        
+    elif code:
+        if not isinstance(code,str): 
+            sys.exit("The code parameter has to be a string!")
+        
+    elif target:
+        if not isinstance(code,str): 
+            sys.exit("The target parameter has to be a string!")
+        
+    elif targetsystem:
+        if not isinstance(code,str): 
+            sys.exit("The targetsystem parameter has to be a string!")
+        
+    else:
+        sys.exit("At least codeableConcept, coding, code, target or targetSystem has to be given!")
+    # end validation and recall of translate in simplier from
+
+    # look for any information from the one ore more generated conceptMaps into con_map_7d
+    match = []
+    unmapped = []
+    if url not in con_map_7d.keys():
+        print('   #ERROR# ConceptMap with URL "'+ url +'" is not loaded to this compiled conceptMap #ERROR#')
+    else:
+        for url_lvl in con_map_7d:
+            if url_lvl == "%" or url_lvl == str(url or ""):#+str(("/?version=" and conceptMapVersion) or ""):
+                for source_lvl in con_map_7d[url_lvl]:
+                    if source_lvl == "%" or not source or source_lvl == source:
+                        for target_lvl in con_map_7d[url_lvl][source_lvl]:
+                            if target_lvl == "%" or not target or target_lvl == target:
+                                for system_lvl in con_map_7d[url_lvl][source_lvl][target_lvl]:
+                                    if system_lvl == "%" or not system or system_lvl == system:#+str(("/?version=" and version) or ""):
+                                        for targetsystem_lvl in con_map_7d[url_lvl][source_lvl][target_lvl][system_lvl]:
+                                            if targetsystem_lvl == "%" or not targetsystem or targetsystem_lvl == targetsystem:
+                                                for code_lvl in con_map_7d[url_lvl][source_lvl][target_lvl][system_lvl][targetsystem_lvl]:
+                                                    if code_lvl == "|" or code_lvl == "~" or code_lvl == "#":
+                                                        unmapped += con_map_7d[url_lvl][source_lvl][target_lvl][system_lvl][targetsystem_lvl][code_lvl]
+                                                    if code_lvl == "%" or not code or code_lvl == code:
+                                                        match += con_map_7d[url_lvl][source_lvl][target_lvl][system_lvl][targetsystem_lvl][code_lvl]                
+                                                    
+    if not match:
+        for one_unmapped in unmapped:
+            tmp_system = ""
+            tmp_version = ""
+            tmp_code = ""
+            tmp_display = ""
+            # replace all "|" values with to translated code (provided from https://hl7.org/fhir/R4B/conceptmap-definitions.html#ConceptMap.group.unmapped.mode)
+            if one_unmapped["concept"]["code"].startswith("|"):
+                tmp_system = system
+                tmp_version = version
+                tmp_code = one_unmapped["concept"]["code"][1:] + code
+            # replace all "~" values with fixed code (provided from https://hl7.org/fhir/R4B/conceptmap-definitions.html#ConceptMap.group.unmapped.mode)
+            elif one_unmapped["concept"]["code"].startswith("~"):
+                tmp_code = one_unmapped["concept"]["code"][1:]
+                tmp_display = one_unmapped["concept"]["display"]
+            elif one_unmapped["concept"]["code"].startswith("#"):
+                # TODO detect recursion like conceptMapA -> conceptMapB -> ConceptMapA -> ...
+                return translate(one_unmapped["concept"]["code"][1:], None, code, system, version, source, 
+                                 coding, codeableConcept, target, targetsystem, reverse, silent)
+            match.append({"equivalence": one_unmapped["equivalence"], 
+                          "concept":{
+                            "system": tmp_system, 
+                            "version": tmp_version, # TODO version of codesystem out of url?
+                            "code": tmp_code,
+                            "display": tmp_display,
+                            "userSelected": False},
+                          "source": one_unmapped["source"]})
+                
+            
+    # see if any match is not "unmatched" or "disjoint"
+    result = False
+    message = ""
+    for one_match in match:
+        if one_match["equivalence"] != "unmatched" and one_match["equivalence"] != "disjoint":
+            result = True 
+
+    if not silent:
+        print('Translation in '+str(round(time.time()-start,3))+' seconds for code "'+code+'" with ConceptMap "'+url+'"')
+    return {"result": result, "message": message, "match": match}
+
+# The con_map_7d is a seven dimensional dictionary, for quickly finding the fitting translation
+# All dimensions except the last are optional, so a explicit NONE value will be used as key and 
+# interpreted as the default key, that always will be fitting, no matter what other keys are fitting.
+# If a version is included (purely optional), than the version will be added with a blank before to the key
+#
+# The 0th dimension is mandatory and stating the ConceptMap with its url (including the version).
+#
+# The 1st dimension is optional and stating the SOURCE valueset (including the version), as one conceptMap can only 
+# have a maximum of one SOURCE, this is reserved for MaLaC-HD ability to process multiple ConceptMaps in one output.
+#
+# The 2nd dimension is optional and stating the TARGET valueset (including the version), as one conceptMap can only 
+# have a maximum of one TARGET, this is reserved for MaLaC-HD ability to process multiple ConceptMaps in one output.
+#
+# The 3th dimension is optional and stating the SYSTEM (including the version) from the source valueset code, as one 
+# code could be used in multiple SYSTEMs from the source valueset to translate. 
+# Not stating a SYSTEM with a code, is not FHIR compliant and not a whole concept, but still a valid conceptmap.
+# As many conceptMaps exists that are worngly using this SYSTEM element as stating the valueset, that should be
+# stated in source, this case will still be supported by MaLaC-HD. Having a conceptMap with a source valueset 
+# and a different SYSTEM valueset will result in an impossible match and an error will not be recognized by MaLaC-HD.
+#
+# The 4th dimension is optional and stating the TARGET SYSTEM (including the version) from the target valueset code, as one 
+# code could be used in multiple SYSTEMs from the target valueset to translate. 
+# Not stating a TARGET SYSTEM with a code, is not FHIR compliant and not a whole concept, but still a valid conceptmap.
+# As many conceptMaps exists that are worngly using this TARGET SYSTEM element as stating the target valueset, that should be
+# stated in target, this case will still be supported by MaLaC-HD. Having a conceptMap with a target valueset 
+# and a different TARGET SYSTEM valueset will result in an impossible match and an error will not be recognized by MaLaC-HD.
+#   
+# The 5th dimension is optional and stating the CODE from the source valueset, as one conceptMap can have none or 
+# multiple CODEs from the source to translate. 
+#
+# The 6th dimension is NOT optional and stating the TARGET CODE from the target valueset. As one source code could be translated 
+# in multiple TARGET CODEs, the whole set have to be returend. 
+# For a translation with explicitly no TARGET CODE, because of an quivalence of unmatched or disjoint, NONE will be returned. 
+#   
+# a minimal example, translating "hi" to "servus": 
+# con_map_7d = {"myConMap": {None: {None: {"hi": {None: {None: ["equivalent", "<coding><code>servus</code></coding>", "https://my.concept.map/conceptMap/my"]}}}}}
+#
+# TODO add a dimension for a specific dependsOn property
+# TODO add a solution for the unmapped element
+con_map_7d = {}
+'''
+
+    def _footer_standalone(self): 
+        self.py_code += '''
+        
+if __name__ == "__main__":
+    parser = init_argparse()
+    args = parser.parse_args()
+    ret = translate(args.code, args.system, args.version, args.source, args.coding, 
+    args.codeableConcept, args.target, args.targetsystem, args.reverse, args.silent)'''
+
+supermod.ConceptMap.subclass = PythonGenerator