From 03570a30e61748bacc3d3362d18a88f9d56e6d37 Mon Sep 17 00:00:00 2001 From: guetebierl Date: Mon, 7 Oct 2024 16:28:10 +0200 Subject: [PATCH] first release v0.1 --- .gitignore | 2 + .idea/.gitignore | 3 + .idea/inspectionProfiles/Project_Default.xml | 14 + .../inspectionProfiles/profiles_settings.xml | 6 + .idea/mdm-to-neo4j.iml | 11 + .idea/misc.xml | 7 + .idea/modules.xml | 8 + .idea/vcs.xml | 6 + LICENSE | 674 ++++++++++++++++++ README.md | 62 ++ docs/.gitkeep | 0 docs/README.md | 12 + docs/uml/.gitignore | 1 + docs/uml/docker.pu | 35 + docs/uml/pu_create.sh | 3 + docs/uml/structure_python.pu | 64 ++ docs/uml/structure_python.svg | 94 +++ requirements.txt | 15 + src/database_connector/__init__.py | 0 src/database_connector/database_connector.py | 384 ++++++++++ src/run.py | 54 ++ src/xml_processor/__init__.py | 0 src/xml_processor/xml_processor.py | 611 ++++++++++++++++ tests/.gitkeep | 0 tests/test_database_connector/__init__.py | 0 .../test_database_connector.py | 24 + tests/xml_creator/__init__.py | 0 tests/xml_creator/xml_crawler.py | 34 + 28 files changed, 2124 insertions(+) create mode 100644 .gitignore create mode 100644 .idea/.gitignore create mode 100644 .idea/inspectionProfiles/Project_Default.xml create mode 100644 .idea/inspectionProfiles/profiles_settings.xml create mode 100644 .idea/mdm-to-neo4j.iml create mode 100644 .idea/misc.xml create mode 100644 .idea/modules.xml create mode 100644 .idea/vcs.xml create mode 100644 LICENSE create mode 100644 README.md create mode 100644 docs/.gitkeep create mode 100644 docs/README.md create mode 100644 docs/uml/.gitignore create mode 100644 docs/uml/docker.pu create mode 100755 docs/uml/pu_create.sh create mode 100644 docs/uml/structure_python.pu create mode 100644 docs/uml/structure_python.svg create mode 100644 requirements.txt create mode 100644 src/database_connector/__init__.py create mode 100644 src/database_connector/database_connector.py create mode 100644 src/run.py create mode 100644 src/xml_processor/__init__.py create mode 100644 src/xml_processor/xml_processor.py create mode 100644 tests/.gitkeep create mode 100644 tests/test_database_connector/__init__.py create mode 100644 tests/test_database_connector/test_database_connector.py create mode 100644 tests/xml_creator/__init__.py create mode 100644 tests/xml_creator/xml_crawler.py diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..c067e50 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +**__pycache__/ +datasource/ diff --git a/.idea/.gitignore b/.idea/.gitignore new file mode 100644 index 0000000..26d3352 --- /dev/null +++ b/.idea/.gitignore @@ -0,0 +1,3 @@ +# Default ignored files +/shelf/ +/workspace.xml diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml new file mode 100644 index 0000000..930c017 --- /dev/null +++ b/.idea/inspectionProfiles/Project_Default.xml @@ -0,0 +1,14 @@ + + + + \ No newline at end of file diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml new file mode 100644 index 0000000..105ce2d --- /dev/null +++ b/.idea/inspectionProfiles/profiles_settings.xml @@ -0,0 +1,6 @@ + + + + \ No newline at end of file diff --git a/.idea/mdm-to-neo4j.iml b/.idea/mdm-to-neo4j.iml new file mode 100644 index 0000000..e1ccf9b --- /dev/null +++ b/.idea/mdm-to-neo4j.iml @@ -0,0 +1,11 @@ + + + + + + + + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..89ba19a --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,7 @@ + + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..83137e9 --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..35eb1dd --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000..85fe2e7 --- /dev/null +++ b/README.md @@ -0,0 +1,62 @@ +# mdm2neo4j +mdm2neo4j imports ODM-XML-files into a Neo4j graph database. + +## Quickstart + +Create a configuration file, storing your details for the database-connection. +E.g. in your home-directory with the name `mdm.conf`. + +```ini +[neo4j] +uri = bolt://localhost:7687 +username = neo4j +password = myfancypassword +``` + +Start the program by providing the location of your configuration-file and the location of the XML-files. + +```sh +python3 src/run.py --conf ~/mdm.conf --files ~/Desktop/datasource +``` + +## Requirements + +- make sure, `python3` is installed +- install the required libraries with `pip install -r requirements.txt` +- download all ODM-XML-files from the [MDM portal]( https://mdm.mi.uni-heidelberg.de/access/register ) and place all XML-files you want to load in one folder +- have a running Neo4j DB (Neo4j version 5) +- create the configuration-file as described in the [Quickstart section](#quickstart) + +## General Structure of Repo + +![](docs/uml/structure_python.svg) + +The two main scripts that do things are `database_connector.py` and `xml_processor.py`. +`run.py` is the "main" script where everything comes together and that is responsible for running everything. + +## Detailled Infos + +The mapping of the odm-xml files to Neo4j is based on specification for ODM version 1.3.2. +The specification document is available on the CDISC website http://www.cdisc.org/odm. + +The mapping includes 18 of 39 elements of the "Study" section (section 3.1.1) of the "General Elements" (section 3) of the ODM specification. +The Neo4j graph has eleven labels: +- Study +- StudyEvent +- Form +- ItemGroup +- Item +- RangeCheck +- CodeList +- CodeListItem +- BasicDefinitions +- MeasurementUnit +- Alias + + +## Tech Docu + +Find the technical documentation in the [`docs`-folder.](docs/) + +## Licence +This program is released under [Version 3 of the GPL or any later version](https://www.gnu.org/licenses/gpl-3.0.en.html). diff --git a/docs/.gitkeep b/docs/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..4aebcd6 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,12 @@ +# mdm2neo4j - Technical Documentation + +Why do I do the things the way I do them? + +## Postprocessing + +### connect postcoordinated aliases +1. `create_fancy_dict` stores data in dictionary from Alias Context, Context follows the pattern +`(.*)\[([0-9],[0-9])\]` with first group () is a string describing the ontology, +second group () is [x,y] where x and y are integers between 0 and 9. +2. `dict_to_list_of_tuples` transforms dictionary to list of tuples such that Cypher can process it +3. `postprocess_connect_postcoord_aliases` creates COMPOSITE-relationships according to list of tuples diff --git a/docs/uml/.gitignore b/docs/uml/.gitignore new file mode 100644 index 0000000..e33609d --- /dev/null +++ b/docs/uml/.gitignore @@ -0,0 +1 @@ +*.png diff --git a/docs/uml/docker.pu b/docs/uml/docker.pu new file mode 100644 index 0000000..0ddc6f8 --- /dev/null +++ b/docs/uml/docker.pu @@ -0,0 +1,35 @@ +@startuml + +title: Dockerisation mdm_to_neo4j +header version: 19.03.2024 + +skinparam shadowing false +skinparam node { + backgroundColor<> #ccccff +} + +node "localhost" { + + folder "input Files" as input { + file "xml" as xml1 + file "xml" as xml2 + } + + node "Container" <> { + component "Python" as py + artifact "mdm_to_neo4j" as mdm + py -- mdm + } + + component "Neo4j" <> as neo4j + + folder "Database Storage" { + database "Neo4j-Database" as db + } + + input <.. mdm + mdm --> neo4j + neo4j -- db +} + +@enduml diff --git a/docs/uml/pu_create.sh b/docs/uml/pu_create.sh new file mode 100755 index 0000000..56c0e33 --- /dev/null +++ b/docs/uml/pu_create.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +plantuml -tsvg . diff --git a/docs/uml/structure_python.pu b/docs/uml/structure_python.pu new file mode 100644 index 0000000..8274eba --- /dev/null +++ b/docs/uml/structure_python.pu @@ -0,0 +1,64 @@ +@startuml + +title: Python-Structure Overview mdm_to_neo4j +header version: 17.09.2024 + +left to right direction + +skinparam nodesep 10 +'skinparam ranksep 20 + +skinparam shadowing false +skinparam node { +} + +together { + actor "User" as user + + file conf [ + **mdm.conf** + ____ + - database connection + ] + + folder "xml-files" as xmls { + collections "*.xml" + } +} + +rectangle "mdm2neo4j" { + package "database_connector" { + component c_neo <> [ + **Neo4jConnection** + ] + } + package "xml_processor" { + component p_xml [ + **XmlProcessor** + ____ + - parse XML file + - logic for inport + ] + } + file run [ + **run.py** + ____ + Parameters: + - path to xml-files + - path to mdm.conf + ] +} + +node "Neo4j DBMS" { + database "neo4j" as db +} + +user --|> run : start +run --> p_xml : 1 Object\nper File +run ..> c_neo : init\nconnection +run -> conf : read-only +run -u-> xmls : read-only +p_xml --> c_neo +c_neo --> db : read/write + +@enduml diff --git a/docs/uml/structure_python.svg b/docs/uml/structure_python.svg new file mode 100644 index 0000000..ef07970 --- /dev/null +++ b/docs/uml/structure_python.svg @@ -0,0 +1,94 @@ +version: 17.09.2024Python-Structure Overview mdm_to_neo4jxml-filesmdm2neo4jdatabase_connectorxml_processorNeo4j DBMSUsermdm.conf- database connection*.xmlrun.pyParameters:- path to xml-files- path to mdm.conf«Singleton»Neo4jConnectionXmlProcessor- parse XML file- logic for inportneo4jstart1 Objectper Fileinitconnectionread-onlyread-onlyread/write \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..7eacb87 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,15 @@ +beautifulsoup4==4.12.3 +lxml==5.1.0 +neo4j==5.18.0 +numpy==2.0.1 +pandas==2.2.2 +python-dateutil==2.9.0.post0 +pytz==2024.1 +six==1.16.0 +soupsieve==2.5 +tzdata==2024.1 + +argparse~=1.4.0 +pip~=24.0 +wheel~=0.41.2 +setuptools~=68.2.0 \ No newline at end of file diff --git a/src/database_connector/__init__.py b/src/database_connector/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/database_connector/database_connector.py b/src/database_connector/database_connector.py new file mode 100644 index 0000000..cffabfa --- /dev/null +++ b/src/database_connector/database_connector.py @@ -0,0 +1,384 @@ +import configparser +import logging + +from neo4j import GraphDatabase, Driver +from pandas import DataFrame +from run import args + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + + +class Neo4jConnection: + # class-level attribute + __instance = None + __uri = None + __username = None + __password = None + + def __new__(cls, *arg, **kwargs): + # definition as singleton + if not cls.__instance: + cls.__instance = super(Neo4jConnection, cls).__new__(cls, *arg, **kwargs) + return cls.__instance + + def __init__(self) -> None: + # Connect to Neo4j database + if not hasattr(self, '__initialized'): + if not self.__uri: + # read config file + conf_file = configparser.ConfigParser() + conf_file.read(args.conf) + + self.__uri = conf_file['neo4j']['uri'] + self.__username = conf_file['neo4j']['username'] + self.__password = conf_file['neo4j']['password'] + + # instance-level attribute for the __connection, will be initialised later + self.__connection = None + # Establish __connection when the instance is created + self.__start_connection() + self.__initialized = True + + def __start_connection(self): + """ + Creating a Driver instance only provides information on how to access the database, but does not actually + establish a __connection. Connection is instead deferred to when the first query is executed. + """ + try: + driver: Driver = GraphDatabase.driver(self.__uri, + auth=(self.__username, self.__password)) # creation of Driver object + driver.verify_connectivity() + self.__connection = driver + logger.debug("Connected to Neo4j database") + return self.__connection + except Exception as e: + logger.error(f"Failed to connect to Neo4j database: {e}") + raise + + def end_connection(self) -> None: + if self.__connection is not None: + self.__connection.close() + logger.debug("Connection to Neo4j database closed") + self.__connection = None + + def create_study_node(self, data: DataFrame): + """ + based on https://neo4j.com/docs/python-manual/current/query-simple/ + """ + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (st:Study {OID: $studyoid, Name: $studyname, Description: $studydescr, Protocol: $studyprotocol})", + studyoid=row['oid'], studyname=row['name'], studydescr=row['descr'], studyprotocol=row["protocol"] + ) + logger.debug(f"Inserted Study node with OID {row['oid']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_studyevent_node(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query("MERGE (:StudyEvent {OID: $oid, Name: $name, Type: $type, StudyOID: $study_oid})", + oid=row['OID'], name=row['Name'], type=row['Type'], study_oid=studyoid + ) + logger.debug(f"Inserted StudyEvent node with OID {row['OID']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_form_node(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:Form {OID: $oid, Name: $name, StudyOID: $studyoid})", + oid=row['OID'], name=row['Name'], studyoid=studyoid) + logger.debug(f"Inserted Form node with OID {row['OID']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_itemgroup_node(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:ItemGroup {OID: $oid, Name: $name, StudyOID: $studyoid})", + oid=row['OID'], name=row['Name'], studyoid=studyoid) + logger.debug(f"Inserted ItemGroup node with OID {row['OID']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_item_node(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:Item {OID: $oid, Name: $name, DataType: $datatype, Question: $question, StudyOID: $studyoid})", + oid=row['itemoid'], name=row['name'], datatype=row['datatype'], question=row['question'], + studyoid=studyoid) + logger.debug(f"Inserted Item node with OID {row['itemoid']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_alias_node(self, data: DataFrame, + studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:Alias {Context: $context, Name: $name, ItemOID: $item, StudyOID: $study})", + context=row['end'], name=row['end_two'], item=row['start'], study=studyoid) + logger.debug(f"Inserted Alias node with name {row['end_two']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_measurementunit_node(self, data: DataFrame): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:MeasurementUnit {OID: $oid, Name: $name, Symbol: $symbol})", + oid=row['oid'], name=row['name'], symbol=row['symbol']) + logger.debug(f"Inserted MeasurementUnit node with name {row['name']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_basedef_node(self, studyoid: str): + conn = self.__connection + try: + conn.execute_query( + "MERGE (:BasicDefinitions {StudyOID: $studyoid})", studyoid=studyoid) + logger.debug(f"Inserted BasicDefinitions node for study {studyoid}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_rangecheck_node(self, data: DataFrame): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:RangeCheck {Comparator: $comp, Constraint: $cons, CheckValue: $val})", + comp=row['comparator'], cons=row['constraint'], val=row['value']) + logger.debug(f"Inserted RangeCheck node") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_codelist_node(self, data: DataFrame, studyoid): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:CodeList {OID: $oid, Name: $name, DataType: $type, StudyOID: $studyoid})", + oid=row['OID'], name=row['Name'], type=row['DataType'], studyoid=studyoid) + logger.debug(f"Inserted CodeList node") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_clitem_node(self, data: DataFrame): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MERGE (:CodeListItem {CodedValue: $cv, Decode: $dc})", + cv=row['codedvalue'], dc=row['decode']) + logger.debug(f"Inserted CodeListItem node") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_study_to_studyevent_rel(self, studyoid: str): + conn = self.__connection + try: + conn.execute_query( + "MATCH (start:Study {OID: $studyoid}), (end:StudyEvent {StudyOID: $studyoid}) MERGE (start)-[:STUDY_HAS_STUDYEVENT]->(end)-[:BACKTRACK]->(start)", + studyoid=studyoid + ) + logger.debug(f"Inserted rels betw Study and StudyEvent") + except Exception as e: + logger.error(f"Failed to populate Neo4j database: {e}") + raise + + def create_itemgroup_to_item_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:ItemGroup {OID: $startoid, StudyOID: $studyoid}), (end:Item {OID: $endoid, StudyOID: $studyoid}) MERGE (start)-[:ITEMGROUP_HAS_ITEM]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endoid=row['end'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw ItemGroup {row['start']} and Item {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_form_to_itemgroup_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:Form {OID: $startoid, StudyOID: $studyoid}), (end:ItemGroup {OID: $endoid, StudyOID: $studyoid}) MERGE (start)-[:FORM_HAS_ITEMGROUP]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endoid=row['end'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw Form {row['start']} and ItemGroup {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_studyevent_to_form_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:StudyEvent {OID: $startoid, StudyOID: $studyoid}), (end:Form {OID: $endoid, StudyOID: $studyoid}) MERGE (start)-[:STUDYEVENT_HAS_FORM]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endoid=row['end'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw StudyEvent {row['start']} and Form {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_item_to_alias_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:Item {OID: $startoid, StudyOID: $studyoid}), (end:Alias {Context: $endcontext, Name: $endname, ItemOID: $startoid, StudyOID: $studyoid}) MERGE (start)-[:ITEM_HAS_ALIAS]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endcontext=row['end'], endname=row['end_two'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw Item {row['start']} and Alias {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_itemgroup_to_alias_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:ItemGroup {OID: $startoid, StudyOID: $studyoid}), (end:Alias {Context: $endcontext, Name: $endname}) MERGE (start)-[:ITEMGROUP_HAS_ALIAS]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endcontext=row['end'], endname=row['end_two'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw ItemGroup {row['start']} and Alias {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_item_to_measurement_rel(self, data: DataFrame, studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:Item {OID: $startoid, StudyOID: $studyoid}), (end:MeasurementUnit {OID: $endoid, Name: $endname}) MERGE (start)-[:ITEM_HAS_MEASUREMENTUNIT]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endoid=row['endoid'], endname=row['endname'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw Item {row['start']} and MeasurementUnit {row['endname']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_basedef_to_study_rel(self, studyoid: str): + conn = self.__connection + try: + conn.execute_query( + "MATCH (start:Study {OID: $studyoid}), (end:BasicDefinitions {StudyOID: $studyoid}) MERGE (start)-[:HAS_BASEDEF]->(end)", + studyoid=studyoid) + logger.debug( + f"Inserted rels betw Study {studyoid} and BasicDefinitions") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_basedef_to_measurement_rel(self, data: DataFrame, + studyoid: str): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:BasicDefinitions {StudyOID: $studyoid}), (end:MeasurementUnit {OID: $endoid, Name: $endname, Symbol: $endsymbol}) MERGE (start)-[:BASEDEF_HAS_MEASUREMENTUNIT]->(end)", + endoid=row['oid'], endname=row['name'], endsymbol=row['symbol'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw BasicDefinitions and MeasurementUnit {row['name']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_item_to_rangecheck_rel(self, data: DataFrame): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:Item {OID: $itemoid}), (end:RangeCheck {Comparator: $comp, Constraint: $cons, CheckValue: $cvalue}) MERGE (start)-[:ITEM_HAS_RANGECHECK]->(end)-[:BACKTRACK]->(start)", + itemoid=row['start'], comp=row['endcomparator'], cons=row['endconstraint'], cvalue=row['endvalue']) + logger.debug( + f"Inserted rels betw Item and RangeCheck") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_item_to_codelist_rel(self, data: DataFrame, studyoid): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:Item {OID: $startoid, StudyOID: $studyoid}), (end:CodeList {OID: $endoid, StudyOID: $studyoid}) MERGE (start)-[:ITEM_HAS_CODELIST]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], endoid=row['end'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw Item {row['start']} and CodeList {row['end']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def create_codelist_to_codelistitem_rel(self, data: DataFrame, studyoid): + conn = self.__connection + try: + for index, row in data.iterrows(): + conn.execute_query( + "MATCH (start:CodeList {OID: $startoid, StudyOID: $studyoid}), (end:CodeListItem {CodedValue: $cv, Decode: $dc}) MERGE (start)-[:CODELIST_HAS_CODELISTITEM]->(end)-[:BACKTRACK]->(start)", + startoid=row['start'], cv=row['endcodedvalue'], dc=row['enddecode'], studyoid=studyoid) + logger.debug( + f"Inserted rels betw CodeList {row['start']} and CodeListItem {row['endcodedvalue']}") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + # postprocessing with cypher queries + def postprocess_set_label_post(self): + conn = self.__connection + try: + conn.execute_query( + "MATCH (n:Alias) WHERE n.Context contains '[' and n.Context contains ',' and n.Context contains ']' set n :Post" + ) + logger.debug(f"Inserted post property in alias nodes") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise + + def postprocess_connect_postcoord_aliases(self, tuples): + conn = self.__connection + try: + conn.execute_query( + """ + UNWIND $data AS row + MATCH (i:Item {OID: row.item_oid}) + WITH row, i + MATCH (a1:Post {StudyOID: row.study_oid, Context: row.ontology + '[' + row.x + ',' + 1 + ']'})--(i) + MATCH (a2:Post {StudyOID: row.study_oid, Context: row.ontology + '[' + row.x + ',' + row.y + ']'})--(i) + WHERE a1 <> a2 + MERGE (a1)-[rel:COMPOSITE]->(a2) + """, data=tuples) + logger.debug(f"Inserted rels btw post-coordinated aliases") + except Exception as e: + logger.error(f"Failed to execute query: {e}") + raise diff --git a/src/run.py b/src/run.py new file mode 100644 index 0000000..6a64945 --- /dev/null +++ b/src/run.py @@ -0,0 +1,54 @@ +import xml_processor.xml_processor as xp +import database_connector.database_connector as db +import argparse +import atexit +import signal +import logging + +MDM2NEO4J_VERSION: str = "0.1" + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + +logger.info('mdm2neo4j v'+MDM2NEO4J_VERSION) + +# define parameters - pass xml files dir and db conf as arguments when running the script +parser = argparse.ArgumentParser() +parser.add_argument('-c', '--conf', required=True, type=str, + help='Configuration file with database connection parameters') +parser.add_argument('-f', '--files', required=True, type=str, help='Directory with xml files') + +# parse parameters +args = parser.parse_args() +xml_file_path = args.files + + +# init db connection + +# TODO + +# define shutdown_hook + +def shutdown_hook(): + # clise db connection + neo4jconnection_object = db.Neo4jConnection() + neo4jconnection_object.end_connection() + logger.info("Connection to Neo4j database closed") + exit() + + +def signal_handler(sig, frame): + shutdown_hook() + + +atexit.register(shutdown_hook) +signal.signal(signal.SIGTERM, signal_handler) +signal.signal(signal.SIGHUP, signal_handler) +signal.signal(signal.SIGQUIT, signal_handler) +signal.signal(signal.SIGABRT, signal_handler) + + +# start mdm2neo4j + +if __name__ == "__main__": + xp.parse_xml(xml_file_path) diff --git a/src/xml_processor/__init__.py b/src/xml_processor/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/xml_processor/xml_processor.py b/src/xml_processor/xml_processor.py new file mode 100644 index 0000000..bf25d44 --- /dev/null +++ b/src/xml_processor/xml_processor.py @@ -0,0 +1,611 @@ +# this script extracts data of an xml file and stores the data in a pandas DataFrame +# the DataFrame is to be given to the node and relationship creator methods from database_connector.py + +import logging +import os + +import pandas as pd +from bs4 import BeautifulSoup +from pandas import DataFrame +import re + +import database_connector.database_connector as db + +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + + +class XmlProcessor: + """ + class handles one XML file + """ + + def __init__(self, xml: BeautifulSoup): + self.xmlfile_to_process = xml + + # helper functions to create multiple data stores for nodes + # general function to create data stores for nodes + @staticmethod + def __extract_data_to_store_for_nodes(soup: object, + tag_name: str, + attributes: list): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :param tag_name: defines for which node label the data is stored, e.g., Alias + :param attributes: one of the lists from above, depending on tag_name, e.g., alias_attributes for Alias node + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes in neo4j + """ + elements = soup.findAll(tag_name) + data = {attr: [] for attr in attributes} + for element in elements: + for attr in attributes: + data[attr].append(element.get(attr)) + element_data = pd.DataFrame(data) + return element_data + + # funtion to create data store for study nodes + @staticmethod + def __get_study_data(soup): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes with label Study in neo4j + """ + # global studyprotocol_list, studydescr_list, studyname_list + study = soup.find('Study') # find 1 tag + studyoid = study.get('OID') + if studyoid == "some OID": + odm = soup.find('ODM') + studyoid_list = [odm.get('Description')] + else: + studyoid_list = [study.get('OID')] + # studyoid_list = [study.get('OID')] + for child in study.GlobalVariables: + if child.name == 'StudyName': + studyname_list = [child.get_text()] + elif child.name == 'StudyDescription': + studydescr_list = [child.get_text()] + elif child.name == 'ProtocolName': + studyprotocol_list = [child.get_text()] + + # studydata = [] + studydata = pd.DataFrame({"oid": studyoid_list, + "name": studyname_list, + "descr": studydescr_list, + "protocol": studyprotocol_list}) + return studydata + + # funtion to create data store for itemdef nodes with question property + @staticmethod + def __itemdef_data_store_with_question(soup): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes with label ItemDef + """ + itemdef = soup.findAll('ItemDef') + itemdef_itemoid = [] + itemdef_names = [] + itemdef_datatypes = [] + itemdef_questions = [] + for item in itemdef: + itemdef_itemoid.append(item.get('OID')) + itemdef_names.append(item.get('Name')) + itemdef_datatypes.append(item.get('DataType')) + + question = item.find('Question') + + translated_text = question.find('TranslatedText', {'xml:lang': 'de'}) + + if not translated_text: + translated_text = question.find('TranslatedText', {'xml:lang': 'en'}) + + itemdef_questions.append(translated_text.text) + + data = pd.DataFrame({"itemoid": itemdef_itemoid, + "name": itemdef_names, + "datatype": itemdef_datatypes, + "question": itemdef_questions}) + return data + + @staticmethod + def __measurementunit_data_store(soup): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes with label ItemDef + """ + measurementunit = soup.findAll('MeasurementUnit') + measurementunit_oid = [] + measurementunit_names = [] + measurementunit_symbols = [] + for item in measurementunit: + measurementunit_oid.append(item.get('OID')) + measurementunit_names.append(item.get('Name')) + + symbol = item.find('Symbol') + + translated_text = symbol.find('TranslatedText', {'xml:lang': 'de'}) + + if not translated_text: + translated_text = symbol.find('TranslatedText', {'xml:lang': 'en'}) + + measurementunit_symbols.append(translated_text.text) + + data = pd.DataFrame({"oid": measurementunit_oid, + "name": measurementunit_names, + "symbol": measurementunit_symbols}) + return data + + @staticmethod + def __get_rangecheck_data(soup): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes with label RangeCheck in neo4j + """ + rangecheck = soup.findAll('RangeCheck') + rc_comparators = [] + rc_constraints = [] + rc_values = [] + for rc in rangecheck: + rc_comparators.append( + rc.get('Comparator', 'no entry')) + rc_constraints.append(rc.get('SoftHard')) + + # Collect all CheckValue elements + checkvalues = [child.get_text() for child in rc.find_all('CheckValue')] + # If no CheckValue elements exist, use default + if not checkvalues: + checkvalues = ['empty list'] + rc_values.append(checkvalues) + + rc_data = pd.DataFrame({"comparator": rc_comparators, + "constraint": rc_constraints, + "value": rc_values}) + return rc_data + + @staticmethod + def __codelistitem_data_store(soup): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :return: pandas Dataframe with data extracted from xml that is needed for creation of nodes with label ItemDef + """ + clitem = soup.findAll('CodeListItem') + clitem_codedvalues = [] + clitem_decodes = [] + for cl in clitem: + clitem_codedvalues.append(cl.get('CodedValue')) + decode = cl.find('Decode') + + translated_text = decode.find('TranslatedText', {'xml:lang': 'de'}) + + if not translated_text: + translated_text = decode.find('TranslatedText', {'xml:lang': 'en'}) + + clitem_decodes.append(translated_text.text) + + data = pd.DataFrame({"codedvalue": clitem_codedvalues, + "decode": clitem_decodes}) + return data + + # general function to create data stores for rels + @staticmethod + def __extract_data_to_store_for_relationships(soup, + def_tag_name: str, + ref_tag_name: str, + def_attr_name: str, + ref_attr_name: str): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :param def_tag_name: startnode label, e.g., label "ItemGroup", input is then "ItemGroupDef" (because of xml structure) + :param ref_tag_name: endnode label, e.g., label "Item", input is then "ItemDef" + :param def_attr_name: startnode property for finding right endnodes (e.g., find all Items that belong to ItemGroup) + :param ref_attr_name: endnode property that is referenced in startnode (e.g., Items referenced in ItemGroup) + :return: pandas Dataframe with data extracted from xml that is needed for creation of relationships in neo4j + """ + end_elements = soup.findAll(ref_tag_name) + data = {'start': [], 'end': []} + for end_element in end_elements: + parents = end_element.parents + for p in parents: + if p.name == def_tag_name: + data['end'].append(end_element.get(ref_attr_name)) + data['start'].append(p.get(def_attr_name)) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_with_two_attributes_to_store_for_relationships(soup, + def_tag_name: str, + ref_tag_name: str, + def_attr_name: str, + ref_attr_name: str, + ref_attr_name_2: str): + """ + :param soup: parsed xml file (parsed with beautiful soup, somewhere) + :param def_tag_name: startnode label, e.g., label "ItemGroup", input is then "ItemGroupDef" (because of xml structure) + :param ref_tag_name: endnode label, e.g., label "Item", input is then "ItemDef" + :param def_attr_name: startnode property for finding right endnodes (e.g., find all Items that belong to ItemGroup) + :param ref_attr_name: endnode property that is referenced in startnode (e.g., Items referenced in ItemGroup) + :return: pandas Dataframe with data extracted from xml that is needed for creation of relationships in neo4j + """ + end_elements = soup.findAll(ref_tag_name) + data = {'start': [], 'end': [], 'end_two': []} + for end_element in end_elements: + parents = end_element.parents + for p in parents: + if p.name == def_tag_name: + data['end'].append(end_element.get(ref_attr_name)) + data['end_two'].append(end_element.get(ref_attr_name_2)) + data['start'].append(p.get(def_attr_name)) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_for_item_to_alias_rels(soup): + end_elements = soup.findAll('Alias') + data = {'start': [], 'endcontext': [], 'endname': []} + for element in end_elements: + parents = end_elements.parents + for p in parents: + if p.name == 'ItemDef': + data['endcontext'].append(element.get('Context')) + data['endname'].append(element.get('Name')) + data['start'].append(p.get('OID')) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_for_to_alias_rels(soup, def_tag_name: str): + end_elements = soup.findAll('Alias') + data = {'start': [], 'endcontext': [], 'endname': []} + for element in end_elements: + parents = end_elements.parents + for p in parents: + if p.name == def_tag_name: + data['endcontext'].append(element.get('Context')) + data['endname'].append(element.get('Name')) + data['start'].append(p.get('OID')) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_for_item_to_measurement_rels(soup): + end_elements = soup.findAll('MeasurementUnitRef') + data = {'start': [], 'endoid': [], 'endname': []} + for end_element in end_elements: + parents = end_element.parents + for p in parents: + if p.name == 'ItemDef': + moid = end_element.get('MeasurementUnitOID') + endnameplaceholder = soup.find('MeasurementUnit', {'OID': moid}) + mname = endnameplaceholder.get('Name') + data['endname'].append(mname) + data['endoid'].append(moid) + data['start'].append(p.get('OID')) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_for_item_to_checkvalue_rels(soup): + end_elements = soup.findAll('RangeCheck') + data = {'start': [], 'endcomparator': [], 'endconstraint': [], 'endvalue': []} + for end_element in end_elements: + parents = end_element.parents + for p in parents: + if p.name == 'ItemDef': + comparator = end_element.get('Comparator', 'null') + soft_hard = end_element.get('SoftHard', 'null') + check_value_elements = [cv.get_text() for cv in end_element.find_all('CheckValue')] + check_value = check_value_elements if check_value_elements else ['null'] + + data['endcomparator'].append(comparator) + data['endconstraint'].append(soft_hard) + data['endvalue'].append(check_value) + + data['start'].append(p.get('OID')) + rels_data = pd.DataFrame(data) + return rels_data + + @staticmethod + def __extract_data_for_codelist_to_codelistitem_rels(soup): + end_elements = soup.findAll('CodeListItem') + data = {'start': [], 'endcodedvalue': [], 'enddecode': []} + for end_element in end_elements: + parents = end_element.parents + for p in parents: + if p.name == 'CodeList': + codedvalue = end_element.get('CodedValue', 'null') + + decode = end_element.find('Decode') + translated_text = decode.find('TranslatedText', {'xml:lang': 'de'}) + + if not translated_text: + translated_text = decode.find('TranslatedText', {'xml:lang': 'en'}) + + data['endcodedvalue'].append(codedvalue) + data['enddecode'].append(translated_text.text) + + data['start'].append(p.get('OID')) + rels_data = pd.DataFrame(data) + return rels_data + + # process xml file with the help of the helper functions + def get_studyoid(self): + return XmlProcessor.__get_study_data(self.xmlfile_to_process)['oid'][0] + + def extract_study_data(self) -> DataFrame: + study_data: DataFrame = XmlProcessor.__get_study_data(self.xmlfile_to_process) + return study_data + + def extract_item_data(self) -> DataFrame: + itemdef_data: DataFrame = XmlProcessor.__itemdef_data_store_with_question(self.xmlfile_to_process) + return itemdef_data + + def extract_studyevent_data(self) -> DataFrame: + studyeventdef_attributes = ['OID', 'Name', 'Type'] + studyeventdef_data: DataFrame = XmlProcessor.__extract_data_to_store_for_nodes(self.xmlfile_to_process, + 'StudyEventDef', + studyeventdef_attributes) + return studyeventdef_data + + def extract_form_data(self) -> DataFrame: + formdef_attributes = ['OID', 'Name'] + formdef_data: DataFrame = XmlProcessor.__extract_data_to_store_for_nodes(self.xmlfile_to_process, + 'FormDef', + formdef_attributes) + return formdef_data + + def extract_itemgroup_data(self) -> DataFrame: + itemgroupdef_attributes = ['OID', 'Name'] + itemgroupdef_data: DataFrame = XmlProcessor.__extract_data_to_store_for_nodes(self.xmlfile_to_process, + 'ItemGroupDef', + itemgroupdef_attributes) + return itemgroupdef_data + + def extract_alias_data(self): + alias_attributes = ['Context', 'Name'] + alias_data: DataFrame = XmlProcessor.__extract_data_to_store_for_nodes(self.xmlfile_to_process, 'Alias', + alias_attributes) + return alias_data + + def extract_measurement_data(self): + measurement_data: DataFrame = XmlProcessor.__measurementunit_data_store(self.xmlfile_to_process) + return measurement_data + + def extract_rangecheck_data(self): + rangecheck_data: DataFrame = XmlProcessor.__get_rangecheck_data(self.xmlfile_to_process) + return rangecheck_data + + def extract_codelist_data(self): + codelist_attributes = ['OID', 'Name', 'DataType'] + codelist_data: DataFrame = XmlProcessor.__extract_data_to_store_for_nodes(self.xmlfile_to_process, 'CodeList', + codelist_attributes) + return codelist_data + + def extract_codelistitem_data(self): + clitem_data: DataFrame = XmlProcessor.__codelistitem_data_store(self.xmlfile_to_process) + return clitem_data + + @property + def extract_itemgroup_to_item_data(self): + itemgroup_to_item_data: DataFrame = XmlProcessor.__extract_data_to_store_for_relationships( + self.xmlfile_to_process, + 'ItemGroupDef', 'ItemRef', + 'OID', 'ItemOID') + return itemgroup_to_item_data + + def extract_item_to_alias_data(self) -> DataFrame: + item_to_alias_data: DataFrame = XmlProcessor.__extract_data_with_two_attributes_to_store_for_relationships( + self.xmlfile_to_process, + 'ItemDef', + 'Alias', + 'OID', + 'Context', + 'Name') + return item_to_alias_data + + def extract_itemgroup_to_alias_data(self) -> DataFrame: + itemgroup_to_alias_data: DataFrame = XmlProcessor.__extract_data_with_two_attributes_to_store_for_relationships( + self.xmlfile_to_process, + 'ItemGroupDef', + 'Alias', + 'OID', + 'Context', + 'Name') + return itemgroup_to_alias_data + + def extract_form_to_itemgroup_data(self) -> DataFrame: + form_to_itemgroup_data: DataFrame = XmlProcessor.__extract_data_to_store_for_relationships( + self.xmlfile_to_process, + 'FormDef', 'ItemGroupRef', + 'OID', 'ItemGroupOID') + return form_to_itemgroup_data + + def extract_studyevent_to_form_data(self) -> DataFrame: + studyevent_to_form_data: DataFrame = XmlProcessor.__extract_data_to_store_for_relationships( + self.xmlfile_to_process, + 'StudyEventDef', + 'FormRef', 'OID', 'FormOID') + return studyevent_to_form_data + + def extract_item_to_measurement_data(self) -> DataFrame: + item_to_measurement_data: DataFrame = XmlProcessor.__extract_data_for_item_to_measurement_rels( + self.xmlfile_to_process) + return item_to_measurement_data + + def extract_item_to_rangecheck_data(self) -> DataFrame: + item_to_rangecheck_data: DataFrame = XmlProcessor.__extract_data_for_item_to_checkvalue_rels( + self.xmlfile_to_process) + return item_to_rangecheck_data + + def extract_item_to_codelist_data(self) -> DataFrame: + item_to_cl_data: DataFrame = XmlProcessor.__extract_data_to_store_for_relationships( + self.xmlfile_to_process, + 'ItemDef', + 'CodeListRef', 'OID', 'CodeListOID') + return item_to_cl_data + + def extract_codelist_to_codelistitem_data(self) -> DataFrame: + cl_to_clitem_data: DataFrame = XmlProcessor.__extract_data_for_codelist_to_codelistitem_rels( + self.xmlfile_to_process) + return cl_to_clitem_data + + @staticmethod + def create_fancy_dict(soup): + data = {} + # Iterate over all Study elements + for study in soup.find_all('Study'): + studyoidcandidate = study.get('OID') + if studyoidcandidate == "some OID": + odm = soup.find('ODM') + study_oid = odm.get('Description') + else: + study_oid = study.get('OID') + + data[study_oid] = {} + + # Iterate over all ItemDef elements + for item in study.find_all('ItemDef'): + item_oid = item.get('OID') + data[study_oid][item_oid] = {} + + # Iterate over all Alias elements + for alias in item.find_all('Alias'): + context = alias.get('Context') + match = re.match(r'(.*)\[([0-9],[0-9])\]', context) + if match: + ontology_context = match.group(1) + xy = match.group(2) + if ',' in xy: + x, y = xy.split(',') + x = int(x) + y = int(y) + else: + x = int(xy) + y = None + else: + ontology_context = context + x = None + y = None + + if ontology_context not in data[study_oid][item_oid]: + data[study_oid][item_oid][ontology_context] = {} + if x is not None: + if x not in data[study_oid][item_oid][ontology_context]: + data[study_oid][item_oid][ontology_context][x] = [] + data[study_oid][item_oid][ontology_context][x].append(y) + return data + + def prepare_tuple_for_postcoord_rels(self): + mydict = XmlProcessor.create_fancy_dict(self.xmlfile_to_process) + return mydict + + +def dict_to_list_of_tuples(mydictionary): + data = [ + { + "study_oid": study_oid, + "item_oid": item_oid, + "ontology": ontology, + "x": x, + "y": y + } + for study_oid, items in mydictionary.items() + for item_oid, ontologies in items.items() + for ontology, x_values in ontologies.items() + for x, y_values in x_values.items() + for y in y_values + ] + return data + + +def parse_xml( + path_to_datafiles): # creates XmlProcessor object for each xml file + neo4jconnection_object = db.Neo4jConnection() + for file in os.listdir(path_to_datafiles): + if file.endswith(".xml"): + filepath = os.path.join(path_to_datafiles, file) + with open(filepath) as fp: + parsed_xml = BeautifulSoup(fp, "xml") + # create XmlProcessor object for parsed_xml files + xmlprocessor_object = XmlProcessor(parsed_xml) + # do stuff with the object + study_oid = xmlprocessor_object.get_studyoid() + + # create nodes + study_data = xmlprocessor_object.extract_study_data() + neo4jconnection_object.create_study_node(study_data) + + itemgroup_data = xmlprocessor_object.extract_itemgroup_data() + neo4jconnection_object.create_itemgroup_node(itemgroup_data, study_oid) + + item_data = xmlprocessor_object.extract_item_data() + neo4jconnection_object.create_item_node(item_data, study_oid) + + studyevent_data = xmlprocessor_object.extract_studyevent_data() + neo4jconnection_object.create_studyevent_node(studyevent_data, study_oid) + + form_data = xmlprocessor_object.extract_form_data() + neo4jconnection_object.create_form_node(form_data, study_oid) + + alias_data = xmlprocessor_object.extract_item_to_alias_data() + neo4jconnection_object.create_alias_node(alias_data, study_oid) + + measurement_data = xmlprocessor_object.extract_measurement_data() + neo4jconnection_object.create_measurementunit_node(measurement_data) + + rangecheck_data = xmlprocessor_object.extract_rangecheck_data() + neo4jconnection_object.create_rangecheck_node(rangecheck_data) + + codelist_data = xmlprocessor_object.extract_codelist_data() + neo4jconnection_object.create_codelist_node(codelist_data, study_oid) + + codelistitem_data = xmlprocessor_object.extract_codelistitem_data() + neo4jconnection_object.create_clitem_node(codelistitem_data) + + if parsed_xml.findAll('BasicDefinitions'): + neo4jconnection_object.create_basedef_node(study_oid) + + logger.info(f"Inserted all nodes for study {study_oid}") + + # create rels + itemgroup_to_item_data = xmlprocessor_object.extract_itemgroup_to_item_data + neo4jconnection_object.create_itemgroup_to_item_rel(itemgroup_to_item_data, study_oid) + + item_to_alias_data = xmlprocessor_object.extract_item_to_alias_data() + neo4jconnection_object.create_item_to_alias_rel(item_to_alias_data, study_oid) + + itemgroup_to_alias_data = xmlprocessor_object.extract_itemgroup_to_alias_data() + neo4jconnection_object.create_itemgroup_to_alias_rel(itemgroup_to_alias_data, study_oid) + + form_to_itemgroup_data = xmlprocessor_object.extract_form_to_itemgroup_data() + neo4jconnection_object.create_form_to_itemgroup_rel(form_to_itemgroup_data, study_oid) + + studyevent_to_form_data = xmlprocessor_object.extract_studyevent_to_form_data() + neo4jconnection_object.create_studyevent_to_form_rel(studyevent_to_form_data, study_oid) + + neo4jconnection_object.create_study_to_studyevent_rel(study_oid) + + item_to_measurement_data = xmlprocessor_object.extract_item_to_measurement_data() + neo4jconnection_object.create_item_to_measurement_rel(item_to_measurement_data, study_oid) + + item_to_rangecheck_data = xmlprocessor_object.extract_item_to_rangecheck_data() + neo4jconnection_object.create_item_to_rangecheck_rel(item_to_rangecheck_data) + + item_to_cl_data = xmlprocessor_object.extract_item_to_codelist_data() + neo4jconnection_object.create_item_to_codelist_rel(item_to_cl_data, study_oid) + + cl_to_clitem_data = xmlprocessor_object.extract_codelist_to_codelistitem_data() + neo4jconnection_object.create_codelist_to_codelistitem_rel(cl_to_clitem_data, study_oid) + + # rels to and from BasicDefinitions node + neo4jconnection_object.create_basedef_to_study_rel(study_oid) + neo4jconnection_object.create_basedef_to_measurement_rel(measurement_data, study_oid) + + logger.info(f"Inserted all rels for study {study_oid}") + + # postprocess + neo4jconnection_object.postprocess_set_label_post() + dictionary = xmlprocessor_object.prepare_tuple_for_postcoord_rels() + datatuple = dict_to_list_of_tuples(dictionary) + neo4jconnection_object.postprocess_connect_postcoord_aliases(datatuple) + + logger.info(f"Post-processing done for study {study_oid}") diff --git a/tests/.gitkeep b/tests/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_database_connector/__init__.py b/tests/test_database_connector/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_database_connector/test_database_connector.py b/tests/test_database_connector/test_database_connector.py new file mode 100644 index 0000000..01dceb3 --- /dev/null +++ b/tests/test_database_connector/test_database_connector.py @@ -0,0 +1,24 @@ +# lassen wir weg +import unittest +from src.database_connector.database_connector import Neo4jConnection + + +class TestNeo4jConnection(unittest.TestCase): + def test_something(self): + self.assertEqual(True, False) # add assertion here + + def test_success(self): + # arrange + uri = "bolt://localhost:7687" + username = "testuser" + password = "wrongpw" + + # act + obj = Neo4jConnection(uri, username, password) + + # assert + # self.assertEqual(, ) # testen ob exception rauskommt + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/xml_creator/__init__.py b/tests/xml_creator/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/xml_creator/xml_crawler.py b/tests/xml_creator/xml_crawler.py new file mode 100644 index 0000000..fa32aff --- /dev/null +++ b/tests/xml_creator/xml_crawler.py @@ -0,0 +1,34 @@ +import unittest +from src.xml_processor.xml_processor import XmlProcessor + + +class TestXmlCrawler(unittest.TestCase): + def test_something(self): + self.assertEqual(True, False) # add assertion here + + def test_get_study_data(self): + self.assertEqual() + + +''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + #def get_study_data(soup): + # study = soup.find('Study') # find 1 tag + # studyoid = study.get('OID') + # if studyoid == "some OID": + # odm = soup.find('ODM') + # studyoid_list = [odm.get('Description')] + # else: + # studyoid_list = [study.get('OID')] + # for child in study.GlobalVariables: + if child.name == 'StudyName': + studyname_list = [child.get_text()] + elif child.name == 'StudyDescription': + studydescr_list = [child.get_text()] + studydata = pd.DataFrame({"oid": studyoid_list, + "name": studyname_list, + "descr": studydescr_list}) + return studydata +''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' + +if __name__ == '__main__': + unittest.main()