Overwatch

Status:

Group Members:

Aaron Joyce
Bryan Quirke
Erik Eviston
Jessa Pajarito
Neil Barry-Murphy

Setup Guide

Using the Flask Application

Activate the virtual environment (Python 2.7 required):

source venv/bin/activate

Run the setup script (First time setup following initial clone - required only once):

bash setup.sh

Restart mongo:

sudo service mongod restart

Run the flask application:

python app.py

(If The Flask Application Fails)
Install necessary requirements with root permissions and restart mongo:

sudo pip install -r requirements.txt

sudo service mongod restart

Now, re-start the application:

python app.py

Navigate to the homepage: http://127.0.0.1:5000/

Logging

Open another terminal in the same directory and execute the following:
Activate the virtual environment:

source venv/bin/activate

Once the app has been started on the previous terminal: - (PML and DINTO Log-file Generation)

tail -f info.log

DDI System Testing Instructions

In-Depth Testing

(Testing methods for all new required features outlined below)

Mock DDI Characterisation Data

• Navigate to the homepage.
• Select Begin Analysis.
• Select coke_and_pepsi.pml. Click Check Validity of Selected File.
• Click Analyse File.
• If successful, click Select Knowledge Base System.
• Click Search DDI Characterization Data.
• Select db_1.csv. Click View Interactions.
• When complete, click Finished - Return to Homepage.

Identify drugs in PML

• Integrated with previous step.

Report un-named PML construct

• Navigate to the homepage.
• Select Begin Analysis.
• Select unnamed_construct.pml. Click Check Validity of Selected File.
• Error will be explained by system, highlighted in red.
• The line number, and type of construct causing the issue will be highlighted by the system.
• The system will not allow progression beyond this point.

Report PML construct name-clash

• Navigate to the homepage.
• Select Begin Analysis.
• Select duplicated_construct.pml. Click Check Validity of Selected File.
• View Results.
• Error will be explained by system, highlighted in red.
• The line number, name and type of construct causing the issue will be highlighted by the system.
• The system will not allow progression beyond this point.

Identify Parallel DDIs

• Navigate to the homepage.
• Select Begin Analysis.
• Select iden_parallel_ddi_2.pml. Click Check Validity of Selected File.
• Refer to peos/pml/drugfinder/pml-test-files/iden_parallel_ddi_2.pml in any editor (such as gedit).
• Two different action constructs refer to two drugs that interact with each other.
• Return to system.
• Click Analyse File.
• If successful, click Select Knowledge Base System.
• Click Search DDI Characterization Data.
• Select db_1.csv. Click View Interactions.
• When complete, click Finished - Return to Homepage.

PML-TX Save PML to File

• This feature cannot be demonstrated as an isolated article.
• The following transformations highlight the actions of this feature.
• In short, all changes made to files that are transformed are saved by the system, a new file is not created.

PML-TX Reorder Sequence

• Refer to peos/pml/drugfinder/pml-test-files/reorder_sequence.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select reorder_sequence.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Reorder Sequence.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/reorder_sequence.pml.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout reorder_sequence.pml

PML-TX Serialise Branch (Naive)

• Refer to peos/pml/drugfinder/pml-test-files/pml_tx_serialize_branch_naive.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select pml_tx_serialize_branch_naive.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Naive Branch Transformation.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/pml_tx_serialize_branch_naive.pml.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout pml_tx_serialize_branch_naive.pml

PML-TX Serialize Branch (Two-Way)

• Refer to peos/pml/drugfinder/pml-test-files/pml_tx_serialize_branch_2_way.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select pml_tx_serialize_branch_2_way.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Two-Way Branch Transformation.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/pml_tx_serialize_branch_2_way.pml.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout pml_tx_serialize_branch_2_way.pml

PML-TX Remove Selections (NOT WORKING)

• Refer to peos/pml/drugfinder/pml-test-files/remove_selection.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select remove_selection.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Remove Selections Transformation.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/remove_selection.pml.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout remove_selection.pml

PML-TX Unroll Iteration

• Refer to peos/pml/drugfinder/pml-test-files/unroll_iteration.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select unroll_iteration.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Unroll Iteration Transformation.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/unroll_iteration.pml.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout unroll_iteration.pml

PML-TX Parallelise Sequence

• Refer to peos/pml/drugfinder/pml-test-files/sequence_parallelisation.pml in any editor (such as gedit).
• Navigate to the homepage.
• Select Begin Analysis.
• Select sequence_parallelisation.pml. Click Check Validity of Selected File.
• Click Analyse File.
• Click Select Transformation Type.
• Click Perform Parallelize Sequence Transformation.
• Ensure to select the radio button, and click Check Validity of Transformation.
• Again, refer to peos/pml/drugfinder/pml-test-files/sequence_parallelisation.pml in your editor.
• Click Reload or equivalent. View changes.
• To view side by side changes, find the file of the same name in peos/pml/drugfinder/duplicate-pml-test-files/.
• This file is an original copy of the file that was just transformed.
• To redo the test, open a new terminal (in the same directory) and execute:

  cd peos/pml/drugfinder/pml-test-files

• From here, revert any changes in git.

  git checkout sequence_parallelisation.pml

Deactivating the Virtual Environment

When finished with analysis of the system, execute:

deactivate

This will disable the virtual environment.

DINTO system (No longer part of the testing branch)

In-Depth Testing

Please note that all explanations are accompanied by images.
See the documentation/testing/testing-process section of this repo for more information.

Successful Tests

• Navigate to the homepage (process described above).
• Select "Begin Analysis".
• Select a pml file (depression.pml or irritable_bowel_syndrome.pml). - (PML file selection)
• depression.pml describes only one drug, and will list all interactions of that drug.
• irritable_bowel_syndrome.pml describes multiple (2) drugs, and will list the interactions between these 2 drugs. - (PML File Loading)
• When a file has been selected, click "Check Validity of Selected File" to continue.
• The next page displayed is the results of a pml file check. - (Running PML Analysis)
• The result will be either valid or invalid. An invalid result will not allow for progression.
• If result is valid, click "Analyse File" to extract the drug information. - (On-Screen PML Reporting)
• You will now be presented with a list containing drug information realting to the title of the pml. (ie - depression will yield a prescription of fluoxetine)
• Click "Search DINTO for Interactions" to continue.
• Next, select the DINTO knowledge base. For the purposes of this test, the only KB is "test_selection.owl". - (Select specific OWL Ontology)
• Select the file, and click "Load Knowledge Base" to continue. - (Load Selected Ontology)
• A list of drug-drug interactions will now be displayed on screen. - (On-Screen DINTO Reporting)
• Click the available links to view drug references for single-instance drug interactions.
• Select "Finished" when analysis is complete. You will be redirected to the homepage.

Tests To Handle Incorrect Input

• Navigate to the homepage (process described above).
• Select "Begin Analysis".
• Select a pml file (pml_format_error.pml, pml_format_correct_analysis_error.pml or pml_format_correct_analysis_correct_no_drug_links.pml).
• pml_format_error.pml has a syntax error in the file. The system will highlight this.
• pml_format_correct_analysis_error.pml describes a pml file that syntactically correct, but the analysis fails as no drug mentions are found. The system will also highlight this.
• pml_format_correct_analysis_correct_no_drug_links.pml describes a test that has a syntactically correct pml file, yields drug or drug names from the analysis, but no links exist in DINTO for these referenced drugs. This test result will again be highlighted by the system.
• The following instructions are the same as above, but various descriptive error messages will be encountered.
• When a file has been selected, click "Check Validity of Selected File" to continue.
• The next page displayed is the results of a pml file check.
• The result will be either valid or invalid. An invalid result will not allow for progression. - (PML Error and Warning highlights)
• If result is valid, click "Analyse File" to extract the drug information.
• You will now be presented with a list containing drug information relating to the title of the pml. (ie - depression will yield a prescription of fluoxetine)
• Click "Search DINTO for Interactions" to continue.
• Next, select the DINTO knowledge base. For the purposes of this test, the only KB is "test_selection.owl".
• Select the file, and click "Load Knowledge Base" to continue.
• If errors exist from any previous section, the relevant DINTO (or PML if previous) errors will be highlighted by the system. - (DINTO Error and Warning highlights)
• Select "Finished" when analysis is complete. You will be redirected to the homepage.

Additional System Analysis

Using the Mongo Database

Installation for Ubuntu 16.04 will be handled by the setup script.
Open a new terminal and execute the following:

Log In to the Mongo shell:

mongo

Switch to the project database:

use app

List all currently available collections:
(Should be empty prior to launching the flask app)

db.getCollectionNames()

List all pml files in the project, for example:

db.dist.files.find()

List all pml files that you have selected as a user:

db.dist.selected.find()

List all pml files that have been analysed:

db.dist.analysis.find()