commit 03570a30e61748bacc3d3362d18a88f9d56e6d37
Author: guetebierl <lea.guetebier@uni-greifswald.de>
Date: Mon Oct 7 16:28:10 2024 +0200
first release v0.1
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 @@
+<component name="InspectionProjectProfileManager">
+ <profile version="1.0">
+ <option name="myName" value="Project Default" />
+ <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+ <option name="ignoredPackages">
+ <value>
+ <list size="1">
+ <item index="0" class="java.lang.String" itemvalue="typing_extensions" />
+ </list>
+ </value>
+ </option>
+ </inspection_tool>
+ </profile>
+</component>
\ 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 @@
+<component name="InspectionProjectProfileManager">
+ <settings>
+ <option name="USE_PROJECT_PROFILE" value="false" />
+ <version value="1.0" />
+ </settings>
+</component>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+ <component name="NewModuleRootManager">
+ <content url="file://$MODULE_DIR$" />
+ <orderEntry type="jdk" jdkName="Python 3.11 (mdm-to-neo4j) (2)" jdkType="Python SDK" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ </component>
+ <component name="PackageRequirementsSettings">
+ <option name="requirementsPath" value="$USER_HOME$/PycharmProjects/mdm-to-neo4j/requirements.txt" />
+ </component>
+</module>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="Black">
+ <option name="sdkName" value="Python 3.11 (mdm-to-neo4j)" />
+ </component>
+ <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.11 (mdm-to-neo4j) (2)" project-jdk-type="Python SDK" />
+</project>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="ProjectModuleManager">
+ <modules>
+ <module fileurl="file://$PROJECT_DIR$/.idea/mdm-to-neo4j.iml" filepath="$PROJECT_DIR$/.idea/mdm-to-neo4j.iml" />
+ </modules>
+ </component>
+</project>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="VcsDirectoryMappings">
+ <mapping directory="" vcs="Git" />
+ </component>
+</project>
\ 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
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+ If, pursuant to or in connection with a single transaction or
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+ Nothing in this License shall be construed as excluding or limiting
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+
+ 12. No Surrender of Others' Freedom.
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+ If conditions are imposed on you (whether by court order, agreement or
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+ 13. Use with the GNU Affero General Public License.
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+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
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+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. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+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:
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+ 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
+<https://www.gnu.org/licenses/>.
+
+ 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
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
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
+
+
+
+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<<Docker>> #ccccff
+}
+
+node "localhost" {
+
+ folder "input Files" as input {
+ file "xml" as xml1
+ file "xml" as xml2
+ }
+
+ node "Container" <<Docker>> {
+ component "Python" as py
+ artifact "mdm_to_neo4j" as mdm
+ py -- mdm
+ }
+
+ component "Neo4j" <<DBMS>> 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 <<Singleton>> [
+ **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 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentScriptType="application/ecmascript" contentStyleType="text/css" height="390px" preserveAspectRatio="none" style="width:1335px;height:390px;" version="1.1" viewBox="0 0 1335 390" width="1335px" zoomAndPan="magnify"><defs/><g><text fill="#888888" font-family="sans-serif" font-size="10" lengthAdjust="spacingAndGlyphs" textLength="95" x="1228" y="10.69">version: 17.09.2024</text><text fill="#000000" font-family="sans-serif" font-size="18" lengthAdjust="spacingAndGlyphs" textLength="359" x="482" y="32.8619">Python-Structure Overview mdm_to_neo4j</text><!--MD5=[337a2b82978a806ce5bcf4ad5fd16aa2]
+cluster xmls--><polygon fill="#FFFFFF" points="76.5,260.1358,141.5,260.1358,148.5,285.2038,180.5,285.2038,180.5,378.1358,76.5,378.1358,76.5,260.1358" style="stroke: #000000; stroke-width: 1.5;"/><line style="stroke: #000000; stroke-width: 1.5;" x1="76.5" x2="148.5" y1="285.2038" y2="285.2038"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="59" x="80.5" y="277.1018">xml-files</text><!--MD5=[45650538d9e692597bc237bf2338e219]
+cluster mdm2neo4j--><rect fill="#FFFFFF" height="275" style="stroke: #000000; stroke-width: 1.5;" width="715" x="326" y="63.1358"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="83" x="642" y="80.1018">mdm2neo4j</text><!--MD5=[d7497fff2e6a9a1d994f1cc59d903d3b]
+cluster database_connector--><polygon fill="#FFFFFF" points="826,158.1358,971,158.1358,978,183.2038,1017,183.2038,1017,280.1358,826,280.1358,826,158.1358" style="stroke: #000000; stroke-width: 1.5;"/><line style="stroke: #000000; stroke-width: 1.5;" x1="826" x2="978" y1="183.2038" y2="183.2038"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="139" x="830" y="175.1018">database_connector</text><!--MD5=[bd29416b877ecfc5c3cef04f79efb9f2]
+cluster xml_processor--><polygon fill="#FFFFFF" points="600,109.1358,706,109.1358,713,134.2038,793,134.2038,793,259.1358,600,259.1358,600,109.1358" style="stroke: #000000; stroke-width: 1.5;"/><line style="stroke: #000000; stroke-width: 1.5;" x1="600" x2="713" y1="134.2038" y2="134.2038"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="100" x="604" y="126.1018">xml_processor</text><!--MD5=[3bec78ca12dc16b09861f7009b8d0a05]
+cluster Neo4j DBMS--><polygon fill="#FFFFFF" points="1137,173.1358,1147,163.1358,1297,163.1358,1297,260.1358,1287,270.1358,1137,270.1358,1137,173.1358" style="stroke: #000000; stroke-width: 1.5;"/><line style="stroke: #000000; stroke-width: 1.5;" x1="1287" x2="1296" y1="173.1358" y2="164.1358"/><line style="stroke: #000000; stroke-width: 1.5;" x1="1137" x2="1287" y1="173.1358" y2="173.1358"/><line style="stroke: #000000; stroke-width: 1.5;" x1="1287" x2="1287" y1="173.1358" y2="270.1358"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="84" x="1171" y="191.1018">Neo4j DBMS</text><!--MD5=[8fc3522a43f8c7199df5e09e5bb0188e]
+entity user--><ellipse cx="128.5" cy="164.1358" fill="#FEFECE" rx="8" ry="8" style="stroke: #A80036; stroke-width: 1.5;"/><path d="M128.5,172.1358 L128.5,199.1358 M115.5,180.1358 L141.5,180.1358 M128.5,199.1358 L115.5,214.1358 M128.5,199.1358 L141.5,214.1358 " fill="none" style="stroke: #A80036; stroke-width: 1.5;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="31" x="113" y="231.6018">User</text><!--MD5=[00b4040e603364f3b74d798c0912c1e4]
+entity conf--><polygon fill="#FEFECE" points="38,78.1358,38,144.2717,219,144.2717,219,88.1358,209,78.1358,38,78.1358" style="stroke: #000000; stroke-width: 1.5;"/><path d="M209,78.1358 L209,88.1358 L219,88.1358 " fill="#FEFECE" style="stroke: #000000; stroke-width: 1.5;"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="71" x="48" y="103.1018">mdm.conf</text><line style="stroke: #000000; stroke-width: 1.5;" x1="39" x2="218" y1="107.2038" y2="107.2038"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="149" x="54" y="126.1697">- database connection</text><!--MD5=[598c7458f910f9705370ab7196b85f6e]
+entity *.xml--><rect fill="#FEFECE" height="35.0679" style="stroke: #000000; stroke-width: 1.5;" width="52" x="104.5" y="310.6358"/><rect fill="#FEFECE" height="35.0679" style="stroke: #000000; stroke-width: 1.5;" width="52" x="100.5" y="306.6358"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="36" x="108.5" y="329.6018">*.xml</text><!--MD5=[983d0794f401e349a629364dfc448d7d]
+entity run--><polygon fill="#FEFECE" points="342,143.1358,342,247.4075,503,247.4075,503,153.1358,493,143.1358,342,143.1358" style="stroke: #000000; stroke-width: 1.5;"/><path d="M493,143.1358 L493,153.1358 L503,153.1358 " fill="#FEFECE" style="stroke: #000000; stroke-width: 1.5;"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="45" x="352" y="168.1018">run.py</text><line style="stroke: #000000; stroke-width: 1.5;" x1="343" x2="502" y1="172.2038" y2="172.2038"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="81" x="358" y="191.1697">Parameters:</text><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="118" x="358" y="210.2376">- path to xml-files</text><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="129" x="358" y="229.3055">- path to mdm.conf</text><!--MD5=[7feca6f6a073612d3294a2c89b6a5708]
+entity c_neo--><rect fill="#FEFECE" height="68.1358" style="stroke: #A80036; stroke-width: 1.5;" width="159" x="842" y="196.1358"/><rect fill="#FEFECE" height="10" style="stroke: #A80036; stroke-width: 1.5;" width="15" x="981" y="201.1358"/><rect fill="#FEFECE" height="2" style="stroke: #A80036; stroke-width: 1.5;" width="4" x="979" y="203.1358"/><rect fill="#FEFECE" height="2" style="stroke: #A80036; stroke-width: 1.5;" width="4" x="979" y="207.1358"/><text fill="#000000" font-family="sans-serif" font-size="14" font-style="italic" lengthAdjust="spacingAndGlyphs" textLength="73" x="880" y="231.1018">«Singleton»</text><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="119" x="857" y="250.1697">Neo4jConnection</text><!--MD5=[be93e3bd3068dc9387925b2bab7c0091]
+entity p_xml--><rect fill="#FEFECE" height="95.2038" style="stroke: #A80036; stroke-width: 1.5;" width="161" x="616" y="147.6358"/><rect fill="#FEFECE" height="10" style="stroke: #A80036; stroke-width: 1.5;" width="15" x="757" y="152.6358"/><rect fill="#FEFECE" height="2" style="stroke: #A80036; stroke-width: 1.5;" width="4" x="755" y="154.6358"/><rect fill="#FEFECE" height="2" style="stroke: #A80036; stroke-width: 1.5;" width="4" x="755" y="158.6358"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacingAndGlyphs" textLength="95" x="631" y="182.6018">XmlProcessor</text><line style="stroke: #A80036; stroke-width: 1.5;" x1="617" x2="776" y1="186.7038" y2="186.7038"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="104" x="637" y="205.6697">- parse XML file</text><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="109" x="637" y="224.7376">- logic for inport</text><!--MD5=[7468467f3b6b392f1d176d828c753b77]
+entity db--><path d="M1188,216.1358 C1188,206.1358 1216.5,206.1358 1216.5,206.1358 C1216.5,206.1358 1245,206.1358 1245,216.1358 L1245,244.2038 C1245,254.2038 1216.5,254.2038 1216.5,254.2038 C1216.5,254.2038 1188,254.2038 1188,244.2038 L1188,216.1358 " fill="#FEFECE" style="stroke: #000000; stroke-width: 1.5;"/><path d="M1188,216.1358 C1188,226.1358 1216.5,226.1358 1216.5,226.1358 C1216.5,226.1358 1245,226.1358 1245,216.1358 " fill="none" style="stroke: #000000; stroke-width: 1.5;"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacingAndGlyphs" textLength="37" x="1198" y="245.1018">neo4j</text><!--MD5=[f271a736112486e7ec41007a5c5ce53c]
+link user to run--><path d="M144.38,195.1358 C176.8,195.1358 256.17,195.1358 321.69,195.1358 " fill="none" id="user->run" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="none" points="321.96,188.1358,341.96,195.1358,321.96,202.1358,321.96,188.1358" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="28" x="266.5" y="191.0328">start</text><!--MD5=[ba94fa49a806251d7bf299e72d969fd6]
+link run to p_xml--><path d="M503.27,195.1358 C537.04,195.1358 576.42,195.1358 610.71,195.1358 " fill="none" id="run->p_xml" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="#A80036" points="615.73,195.1358,606.73,191.1358,610.73,195.1358,606.73,199.1358,615.73,195.1358" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="49" x="534" y="173.0328">1 Object</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="43" x="537" y="190.7389">per File</text><!--MD5=[0a3e5cb278b49f4eda44a0ba082371fa]
+link run to c_neo--><path d="M496.68,247.2158 C525.06,264.4258 558.71,281.3958 592,290.1358 C681.85,313.7158 710.61,311.5558 801,290.1358 C821.62,285.2458 842.72,276.2258 861.35,266.6258 " fill="none" id="run->c_neo" style="stroke: #A80036; stroke-width: 1.0; stroke-dasharray: 7.0,7.0;"/><polygon fill="#A80036" points="866.03,264.1758,856.2025,264.824,861.6045,266.5028,859.9256,271.9048,866.03,264.1758" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="19" x="687" y="268.0328">init</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="67" x="663" y="285.7389">connection</text><!--MD5=[8a7386d18f110db2ce9aedfd23e4f484]
+link run to conf--><path d="M341.98,172.2558 C305.61,161.7958 262.23,149.3158 224.19,138.3758 " fill="none" id="run->conf" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="#A80036" points="219.09,136.9058,226.6498,143.2185,223.8987,138.2757,228.8415,135.5246,219.09,136.9058" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="57" x="252" y="144.0328">read-only</text><!--MD5=[c6c1c7183ed8c16cfda3e0bc9fd1c103]
+reverse link xmls to run--><path d="M180.8434,370.3673 C181.589,370.3094 182.3383,370.2482 183.0909,370.1838 C184.5962,370.0548 186.115,369.9125 187.6447,369.7559 C193.7637,369.1293 200.0577,368.2729 206.3622,367.121 C218.9713,364.8171 231.6225,361.3308 243,356.1358 C297.1,331.4358 346.28,284.3458 379.25,247.4458 " fill="none" id="xmls<-run" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="#A80036" points="180.8434,370.3673,190.1263,373.658,185.8284,369.98,189.5065,365.6821,180.8434,370.3673" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="57" x="252" y="311.0328">read-only</text><!--MD5=[bb19df8b27ca915d940688a46e47b57a]
+link p_xml to c_neo--><path d="M777.06,207.6258 C796.44,210.6658 817.21,213.9258 836.77,216.9958 " fill="none" id="p_xml->c_neo" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="#A80036" points="841.72,217.7658,833.4445,212.4259,836.7798,216.9948,832.2108,220.3302,841.72,217.7658" style="stroke: #A80036; stroke-width: 1.0;"/><!--MD5=[168b4436ec304b879fe0277419ebc878]
+link c_neo to db--><path d="M1001.02,230.1358 C1060.47,230.1358 1139.12,230.1358 1182.77,230.1358 " fill="none" id="c_neo->db" style="stroke: #A80036; stroke-width: 1.0;"/><polygon fill="#A80036" points="1187.91,230.1358,1178.91,226.1358,1182.91,230.1358,1178.91,234.1358,1187.91,230.1358" style="stroke: #A80036; stroke-width: 1.0;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacingAndGlyphs" textLength="62" x="1058" y="226.0328">read/write</text><!--MD5=[5ab261c7ae6e0a3bf4e4d0c104556701]
+@startuml
+
+title: Python-Structure Overview mdm_to_neo4j
+header version: 17.09.2024
+
+left to right direction
+
+skinparam nodesep 10
+
+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 <<Singleton>> [
+ **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
+
+PlantUML version 1.2020.02(Sun Mar 01 11:22:07 CET 2020)
+(GPL source distribution)
+Java Runtime: OpenJDK Runtime Environment
+JVM: OpenJDK 64-Bit Server VM
+Java Version: 17.0.12+7-Debian-2deb12u1
+Operating System: Linux
+Default Encoding: UTF-8
+Language: en
+Country: GB
+--></g></svg>
\ 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()