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=Lab 1: Getting started with Pycharm, Python and RDFlib=
==Topics==
# Prepare for programming knowledge graphs with rdflib in Python.
# Get started with basic RDF programming.


==Topics==  
==Useful materials==
Installation of and introduction to Python, Pycharm, Pip and RDFlib.
VSCode:
* [https://code.visualstudio.com/docs/python/python-tutorial Getting Started with Python in VS Code]
* [https://code.visualstudio.com/docs/python/environments# Using Python environments in VS Code] (pip is easiest to start with)


'''PyCharm''' is a Python Integrated Development Environment (IDE) that can be used for writing python code.
RDFlib:
* [https://rdflib.readthedocs.io/en/stable/gettingstarted.html Intro to RDFlib]
* [https://rdflib.readthedocs.io/en/stable/intro_to_creating_rdf.html  Intro to creating triples]
* [https://rdflib.readthedocs.io/en/stable/intro_to_parsing.html Serialising and parsing]
* [https://www.youtube.com/watch?v=sCU214rbRZ0 8 min introduction video to RDFlib]


'''Pip''' is used to easily install additional python packages for your coding environment.
Lab Presentations:
* [https://docs.google.com/presentation/d/1blXlTTTsL8jqeV5sRLhQuZ-nssNZqH_bjSgjj-kougE/edit?usp=sharing Lab 1 - RDF Presentation]


'''RDFLib''' is a Python package for working with RDF. With this we can create RDF graphs, parse and serialize RDF, perform SPARQL queries on graphs and more.
RDFlib classes/interfaces and methods:
* Graph (add, close, and perhaps remove methods)
* URIRef
* Literal
* Namespace


==Tasks==
==Tasks==
===Install Python, Pip, VSCode, and RDFlib===
'''1)''' You need to have Python version >= 3.7 on your computer. Use the command ''python --version'' in a command/terminal window to check. You can download Python and Pip [https://www.python.org/downloads/ here]. To ensure you have the most recent Pip, you can do
python -m pip install --upgrade pip


You likely already have '''Python''' installed on your computer (it comes with MAC for instance). To find out, type 'python' in  the commandline on windows or type 'python --version' in the terminal on your MAC.
'''2)''' You need to have an Integrated Development Environment (IDE) that supports Python. If you are unsure, you can download the free and open source Visual Studio Code (VSCode) [https://code.visualstudio.com/Download here].
If you don't already have Python, download and install the Python for your operative system [https://www.python.org/downloads/ here.]
We recommend downloading the most recent version.
 
If you are already using a different Python IDE than Pycharm that you are comfortable with, then you are free to use that program instead.
 
Otherwise Download and Install the free and open source '''Pycharm Community Edition''' IDE [https://www.jetbrains.com/pycharm/download/ here.]


'''3)''' Create a folder for INFO216. Start VSCode and ''create a workspace'' in the file menu (File Menu --> Save Workspace As) and save it in your folder. Afterwards, on the left side of VSCode, click on the document icon (explorer). Click Open Folder, and open your INFO216 folder. Create a new file with ''.py'' extension.


'''Pip On Windows:'''  
'''4)''' You will be asked to install the Python extension, install it. If you weren't asked, on the left side of VSCode click on the 4 cubes (extension manager). Within here search for Microsoft's Python extension and install it.  
Download pip here: https://bootstrap.pypa.io/get-pip.py. (Right click on this link and click "Save link as". You can save it to you desktop or somewhere else if you would like)


Open a command prompt and navigate to the folder containing get-pip.py. (e.g enter 'cd Desktop' to get to the desktop)
'''5)''' If you don't have your terminal open, go to the top menu and click on terminal, and then ''New Terminal''. Check where your terminal window is currently located. The bottom line starting with ''PS'' or ''(base)'' shows where it's located. If you added the folder earlier, then you should be located in your INFO216 folder. However, if the destination after PS is not your INFO216 folder, you need to locate to this folder. You can move through folders with the ''cd'' command in the terminal. For instance, if you are at ''PS C:\Users\YourName>'' and your INFO216 folder is at your desktop, you could type the following ''cd .\Desktop\INFO216\''.   


Now run the following command in the promt 'python get-pip.py'
'''6)''' If you are correctly located, type in the following command into your terminal window


'''Pip On Mac:'''
(Windows)
py -3 -m venv .venv
.venv\scripts\activate


Open the terminal and first run: 'curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py'
(Mac / Linux)
python3 -m venv .venv
source .venv/bin/activate


Now run this: 'python get-pip.py'
'''7)''' If you get the message ''"... is not digitally signed. You cannot run this script on the current system."'' copy and paste the following in the terminal, and repeat step 6:
Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope Process


'''8)''' This should now have created a virtual environment in your folder called ''.venv''. In the bottom right corner you will receive a notification asking your to select the new environment for the workspace folder, select yes. You should now see a ''(.venv)'' in front of PS/(base) in the terminal window. Your virtual environment should now automatically be selected when you open your workspace. However, sometimes you might need to open a new terminal for the (.venv) to appear. 


'''RDFlib'''  
'''9)''' In the terminal, type the following to install RDFlib:
pip install rdflib


Using the Pycharm terminal, install RDFlib by simply entering: pip install rdflib
'''10)''' You might need to close and reopen VSCode for RDFlib to work. You can now ''import rdflib'' into your ''.py'' file, or import specific classes/inferfaces such as ''from rdflib import Namespace, Graph''.


Start Pycharm and create a new project with a new .py file.
'''11)''' Right click in your code and click "Run Current File in Interactive Window". When running your program for the first time, you might be asked to install ''ipykernel package'', install it.  


To import rdflib to your .py file, write 'import rdflib' at the top of the file.  
===Programming tasks===
Alternatively to import certain modules of rdflib, you can write e.g 'from rdflib import Graph, URIRef
'''Task:'''  
Represent the sentences below as triples. Note that some sentences can result in several triples.
* The Mueller Investigation was lead by Robert Mueller.
** It involved Paul Manafort, Rick Gates, George Papadopoulos, Michael Flynn, Michael Cohen, and Roger Stone.
* Paul Manafort was business partner of Rick Gates.
** He was campaign chairman for Donald Trump
** He was charged with money laundering, tax evasion, and foreign lobbying.
** He was convicted for bank and tax fraud.
** He pleaded guilty to conspiracy.
** He was sentenced to prison. 
** He negotiated a plea agreement.
* Rick Gates was charged with money laundering, tax evasion and foreign lobbying.
** He pleaded guilty to conspiracy and lying to FBI.


'''Task:''' Write a program that creates an RDF graph and adds the triples you just created.


'''Coding Tasks'''
For the URIs, you can just use an example path like ''http://example.org/''.
So if you want to represent Donald Trump, the URI could be ''http://example.org/Donald_Trump'', and you can create the resource like this:
from rdflib import URIRef
donaldTrump = URIRef('http://example.org/Donald_Trump')


When solving the coding tasks you can look at the readings below.
You can even use a Namespace so you don't have to write the full URI every time:
Use the Classes/interfaces and methods listed at the bottom of the page.  
from rdflib import Namespace
ex = Namespace('http://example.org/')
donaldTrump = ex.Donald_Trump


'''Task:''' Use the ''serialize'' method of ''rdflib.Graph'' to write out the model in different formats (on screen or to file):
* Turtle (format='ttl')
* N-Triple (format='nt')
* JSON-LD (format='json-ld')
* RDF-XML (format='xml')


'''1.''' Write a program that creates an RDF graph containing the triples from the following sentences. Note that one sentence could result in more than one triple.
Which one is easiest to read? What are the pros and cons of the different formats?
We will look more at some of them later in the course!


* Cade is married to Mary
'''Task:''' Use the simple [https://www.ldf.fi/service/rdf-grapher online RDF grapher] to visualise your model. :isSemantic offers [https://issemantic.net/rdf-visualizer a more advanced RDF visualiser] that you can also test if you want.
* Cade is 27 years old
* The capital of France is Paris
* Marys interests include hiking, chocolate and biology
* Paris is a City in France
* Cade and Mary are people


'''Task:''' Loop through the triples in the model to print out all triples that have ''pleading guilty'' as predicate. If you have been inconsistent about some predicate or other term, you can first write loops that correct wrong terms everywhere in the model. (''Tip:'' to correct a term in a model, you typically have to first ''remove'' the old triple and then ''add'' a new one.)


==If you have more time...==
==If you have more time...==
If you have more time you can continue extending your graph with some of the stuff from lab 2:
'''Task:''' If you have more time you can continue extending your graph:
''"Cade Tracy lives in 1516 Henry Street, Berkeley, California 94709, USA. He has a B.Sc. in biology from the University of California, Berkeley from 2011. His interests include birds, ecology, the environment, photography and travelling. He has visited Canada and France."''
* Michael Cohen was Donald Trump's attorney.
Try to use as many different methods as possible to create the triples.
** He pleaded guilty for lying to Congress.
 
* Michael Flynn was adviser to Donald Trump.
==Documentation and other useful reading==
** He pleaded guilty for lying to the FBI.
If needed here is an introduction of how to create projects and python files in Pycharm [https://www.jetbrains.com/help/pycharm/creating-and-running-your-first-python-project.html Pycharm - Tutorial by jetbrains.com].
** He negotiated a plea agreement.
 
[https://rdflib.readthedocs.io/en/stable/index.html# RDFLib Documentation]- Todays focus are the following:
* [https://rdflib.readthedocs.io/en/stable/gettingstarted.html Intro to RDFlib]
* [https://rdflib.readthedocs.io/en/stable/intro_to_creating_rdf.html  Intro to creating triples]
 
Additional recommended in depth documentation:
* [https://rdflib.readthedocs.io/en/stable/rdf_terms.html RDF Terms]
* [https://rdflib.readthedocs.io/en/stable/namespaces_and_bindings.html Namespaces and Bindings]
 
[[:File:S01-KG-8.pdf | Slides from the lecture]]


==Relevant RDFlib interfaces (and methods)==
'''Task:''' According to [https://www.pbs.org/wgbh/frontline/article/the-mueller-investigation-explained-2/ this FRONTLINE article], Gates', Cohen's and Flynn's lying were different and are described in different detail. How can you modify your knowledge graph to account for this?
import [https://rdflib.readthedocs.io/en/stable/py-modindex.html rdflib]:
*Graph (add)
*URIRef
*Bnode
*Literal
*NameSpace
*RDF, FOAF


All RDFlib modules can be found [https://rdflib.readthedocs.io/en/stable/py-modindex.html here]
'''Task:''' Write a method (function) that submits your model to https://www.ldf.fi/service/rdf-grapher for rendering and saves the returned image to file.
Browser search (often Ctrl-F) is useful here to find the module that you want.

Latest revision as of 13:18, 19 January 2024

Topics

  1. Prepare for programming knowledge graphs with rdflib in Python.
  2. Get started with basic RDF programming.

Useful materials

VSCode:

RDFlib:

Lab Presentations:

RDFlib classes/interfaces and methods:

  • Graph (add, close, and perhaps remove methods)
  • URIRef
  • Literal
  • Namespace

Tasks

Install Python, Pip, VSCode, and RDFlib

1) You need to have Python version >= 3.7 on your computer. Use the command python --version in a command/terminal window to check. You can download Python and Pip here. To ensure you have the most recent Pip, you can do

python -m pip install --upgrade pip

2) You need to have an Integrated Development Environment (IDE) that supports Python. If you are unsure, you can download the free and open source Visual Studio Code (VSCode) here.

3) Create a folder for INFO216. Start VSCode and create a workspace in the file menu (File Menu --> Save Workspace As) and save it in your folder. Afterwards, on the left side of VSCode, click on the document icon (explorer). Click Open Folder, and open your INFO216 folder. Create a new file with .py extension.

4) You will be asked to install the Python extension, install it. If you weren't asked, on the left side of VSCode click on the 4 cubes (extension manager). Within here search for Microsoft's Python extension and install it.

5) If you don't have your terminal open, go to the top menu and click on terminal, and then New Terminal. Check where your terminal window is currently located. The bottom line starting with PS or (base) shows where it's located. If you added the folder earlier, then you should be located in your INFO216 folder. However, if the destination after PS is not your INFO216 folder, you need to locate to this folder. You can move through folders with the cd command in the terminal. For instance, if you are at PS C:\Users\YourName> and your INFO216 folder is at your desktop, you could type the following cd .\Desktop\INFO216\.

6) If you are correctly located, type in the following command into your terminal window

(Windows)

py -3 -m venv .venv
.venv\scripts\activate

(Mac / Linux)

python3 -m venv .venv
source .venv/bin/activate

7) If you get the message "... is not digitally signed. You cannot run this script on the current system." copy and paste the following in the terminal, and repeat step 6:

Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope Process

8) This should now have created a virtual environment in your folder called .venv. In the bottom right corner you will receive a notification asking your to select the new environment for the workspace folder, select yes. You should now see a (.venv) in front of PS/(base) in the terminal window. Your virtual environment should now automatically be selected when you open your workspace. However, sometimes you might need to open a new terminal for the (.venv) to appear.

9) In the terminal, type the following to install RDFlib:

pip install rdflib

10) You might need to close and reopen VSCode for RDFlib to work. You can now import rdflib into your .py file, or import specific classes/inferfaces such as from rdflib import Namespace, Graph.

11) Right click in your code and click "Run Current File in Interactive Window". When running your program for the first time, you might be asked to install ipykernel package, install it.

Programming tasks

Task: Represent the sentences below as triples. Note that some sentences can result in several triples.

  • The Mueller Investigation was lead by Robert Mueller.
    • It involved Paul Manafort, Rick Gates, George Papadopoulos, Michael Flynn, Michael Cohen, and Roger Stone.
  • Paul Manafort was business partner of Rick Gates.
    • He was campaign chairman for Donald Trump
    • He was charged with money laundering, tax evasion, and foreign lobbying.
    • He was convicted for bank and tax fraud.
    • He pleaded guilty to conspiracy.
    • He was sentenced to prison.
    • He negotiated a plea agreement.
  • Rick Gates was charged with money laundering, tax evasion and foreign lobbying.
    • He pleaded guilty to conspiracy and lying to FBI.

Task: Write a program that creates an RDF graph and adds the triples you just created.

For the URIs, you can just use an example path like http://example.org/. So if you want to represent Donald Trump, the URI could be http://example.org/Donald_Trump, and you can create the resource like this:

from rdflib import URIRef

donaldTrump = URIRef('http://example.org/Donald_Trump')

You can even use a Namespace so you don't have to write the full URI every time:

from rdflib import Namespace

ex = Namespace('http://example.org/')
donaldTrump = ex.Donald_Trump

Task: Use the serialize method of rdflib.Graph to write out the model in different formats (on screen or to file):

  • Turtle (format='ttl')
  • N-Triple (format='nt')
  • JSON-LD (format='json-ld')
  • RDF-XML (format='xml')

Which one is easiest to read? What are the pros and cons of the different formats? We will look more at some of them later in the course!

Task: Use the simple online RDF grapher to visualise your model. :isSemantic offers a more advanced RDF visualiser that you can also test if you want.

Task: Loop through the triples in the model to print out all triples that have pleading guilty as predicate. If you have been inconsistent about some predicate or other term, you can first write loops that correct wrong terms everywhere in the model. (Tip: to correct a term in a model, you typically have to first remove the old triple and then add a new one.)

If you have more time...

Task: If you have more time you can continue extending your graph:

  • Michael Cohen was Donald Trump's attorney.
    • He pleaded guilty for lying to Congress.
  • Michael Flynn was adviser to Donald Trump.
    • He pleaded guilty for lying to the FBI.
    • He negotiated a plea agreement.

Task: According to this FRONTLINE article, Gates', Cohen's and Flynn's lying were different and are described in different detail. How can you modify your knowledge graph to account for this?

Task: Write a method (function) that submits your model to https://www.ldf.fi/service/rdf-grapher for rendering and saves the returned image to file.