Getting Started with PBJ - apache/ctakes GitHub Wiki

• Apache cTAKES
• Python virtual environment
• Apache Artemis broker

1. Download Apache ActiveMQ Artemis here: https://activemq.apache.org/components/artemis/download/
   
2. In a terminal, navigate to the apache-artemis folder
   
3. Navigate into bin, then use these commands ./bin/artemis create [name of your broker] for Mac and Linux or bin\artemis create [name of your broker] for Windows

• You will be prompted to create a username and password, as well as --allow-anonymous, Press Y for this option

You should now have an Artemis broker and can now run PBJ

For more information see apache-artemis documentation.

For this example we will use the Piper File Submitter. You can also run the example using a shell script with a cTAKES installation if you prefer.

1. Start the Piper File Submitter.
   
2. Load the piper file in the ctakes-examples module called PbjSentencePrinter.

• The file path is [ctakes-examples/src/user/resources/org/apache/ctakes/examples/pipeline/PbjSentencePrinter.piper
  • The GUI should have loaded the piper file and appear as below.
    

3. In the parameter table, set parameter values for your system.

Parameter Name	Option	Value
InputDirectory	-i	Location for input.
OutputDirectory	-o	Location for output.
ArtemisBroker	-a	Location of your Artemis Broker.
VirtualEnv	-v	Location of your Python virtual environment.
PipPbj	--pipPbj	run python pip on PBJ.

An example from my system is below.
The value for input directory is set to the example notes distributed with cTAKES:
ctakes-examples/src/user/resources/org/apache/ctakes/examples/notes/annotated/
The first time you run PBJ you should use 'yes' to pip its code and obtain required libraries.

4. Click the RUN button.

• You should see run output similar to that in the image below.
  
• When the run is complete you should see output similar to that in the image below.

NOTE Any PBJ pipeline is composed of 2 or more sub-pipelines. For the PBJ Sentence Printer there are 3.
What you see in the GUI is only the output of the first sub-pipeline.
The first sub-pipeline may finish long before the second and third complete, so do not be surprised if a Python process or second cTAKES (java) process is still running. The run time required by these processes is dependent upon their complexity.
You can check the progress of sub-pipelines (and therefore the entire PBJ pipeline) by inspecting the output for completion.

Any PBJ run will create 4 log files in your specified output directory.

ctakes_artemis_start.log will contain run information from the Apache Artemis broker.
ctakes_artemis_stop.log may contain additional run information from the broker, but is normally empty.
ctakes_PbjThirdStep.log contains output from the cTAKES pipeline that ran after the Python pipeline.
sentence_printer_pipeline.log contains output from the Python pipeline.

sentence_printer_pipeline.log should have contents similar to:

ctakes_PbjThirdStep.log should have contents similar to:

The PBJ Sentence Printer example places per-document output in three directories:
html/
table/
text/

As the Python pipeline of the PbjSentencePrinter example only detects sentences, the best output files for inspection are those in the text/ directory.
Your directory should have contents similar to:

An text file should have contents similar to:

• On some systems cTAKES cannot properly start an Artemis broker. You must start one manually.

1. Open a terminal and navigate to your Artemis installation.
2. Execute the command bin/artemis run.

• You may see messages at the end of a PBJ run indicating that there were problems stopping the Artemis broker. Normally these can be ignored, but check your system for running instances of a broker. If all sub-pipelines of your PBJ pipeline have finished you can manually stop the broker.