@reubano yes. I refactored based on the comments.

@lamby 😆 the RST syntax is even sicker

@reubano I have done the changes. The tables are now appearing. It's quite _strict_ though.

@reubano yes it is! Let me format the tables for this files with the inline `rst` and also update that format in the algorithms template file.

## Description Add algorithm documentation pages to the docs table of contents ## Reference to official issue Addresses issue #258 ## Motivation and Context Adds algorithms documentation to the `toc tree` ## How Has This Been Tested? - `docker-compose -f local.yml up` - Navigate to [http://localhost:8002/](http://localhost:8002) - The table of contents has the **Algorithms** section under **Code Documentation** ## Not done The algorithm doc files are in `markdown`. Most of them have tables and they're not well displayed on the pages (parsed as paragraphs 🙄 ). Some searching brought me across to this [stackoverflow answer](https://stackoverflow.com/a/44463828/4444629). Basically, to display the tables the best approach is to use `reST` mark up files. ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

@lamby I have fixed the conflicts now 😄

@isms I came across a similar error doing the steps and I fixed it with `$ docker-compose -f local.yml run interface python manage.py makemigrations` `$ docker-compose -f local.yml run interface python manage.py migrate`

## Description Move serializers in the `interface` app into a single file for each directory ## Reference to official issue Addresses issue #201 ## Motivation and Context Makes the app structure cleaner and concise ## How Has This Been Tested? `interface.backend.cases` and `interface.backend.images` have a `serializers.py` file that holds all the respective serializers previously situated in their `models.py` files. ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

@lamby it's updated now 😃

Updates the short git hash that matches the current version of the code in the navbar ## Description This allows the navbar to have the short version of the current commit hash from HEAD. ## Reference to official issue Fixes issue #244 ## Motivation and Context Get the hash of the latest commit as the display instead of a static value. ## How Has This Been Tested? - Run `docker-compose -f local.yml build` - Run `docker-compose -f local.yml up` - View the application UI on [http://localhost:8080/#/](http://localhost:8080/#/) - Open another terminal in the root of your project repo and run `git rev-parse --short HEAD` - The hash on the top right side of the navbar should be the same to the value of the previous step ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

I have some here too: 1. What would you like improved/ changed in your current workflow using tools with standard PACS software package with the current workflow in the concept-to-clinic project? 2. In the lung cancer screening report, is there information in the standard template that is missing and you would want in the report generated by concept-to-clinic project (or omitted)? If there is, which info and why? 3. In the event the tool being built would allow multiple algorithm results and reports were based on a given algorithm, how would that impact the final decision a clinician makes about the cancer detection?

@reubano interestingly, I've done the build without any errors from the current master branch. **OS** : Manjaro Linux **Docker version**: 17.10.0-ce, build f4ffd2511c My suggestion would be you try with upgraded docker?

@lamby updated with some sample files

@lamby I think the update should be clearer on the changed files now 😄

hi @lamby yes. I meant to squash it into one commit.

Clicking on the report and export section, you have an export functionality that downloads the page as a pdf file. ## Description Create a pdf file of the section of the site in the **Report and Export** section ## Reference to official issue Addresses issue #205 ## Motivation and Context This feature allows downloading of the page information. ## How Has This Been Tested? - Load [http://localhost:8080/](http://localhost:8080/) - Click on the **Report and Export** menu section - Click on the **Export** button - It should download the page information in pdf format ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

Loading [http://localhost:8080/](http://localhost:8080) throws an `IsADirectoryError: [Errno 21] Is a directory: '/'` ## Description The endpoint is called every time the front end loads. Since the `dicom.readfile()` method is an IO op, I do a `try/except` to catch the `IOError` 21. As it is, this error is only anticipated on page load because there's no default path to a dicom file. I return an 'empty' response back so that the error is handled on the server-side and presents the client side an opportunity to handle it too. ### To handle the empty response from the server. `Cornerstone` throws errors if handed empty fields on the front end. Since the functions trigger calls to the server endpoint on load (I am assuming this is because of the `async/await` computed functions -- please correct my reasoning here if I'm wrong) and has nothing to display, catering for instances of empty values mitigates these unnecessary errors. Check the changes in [OpenDICOM.vue file](https://github.com/musale/concept-to-clinic/blob/fb39d63d387f2706c6e69792c3739bf61f76506f/interface/frontend/src/components/open-image/OpenDICOM.vue). ## Reference to official issue Fixes issue #206 ## Motivation and Context This change removes the error logs for `IsADirectoryError` and also handles instances where a dicom file is not found. ## How Has This Been Tested? - Load [http://localhost:8080/](http://localhost:8080) - There should be no error traceback ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

## Description Create new files to handle the index pages of the `prediction` and `interface` modules inside `docs`. Generally, `sphinx-api` on these two modules auto generates the documentation. Ignore the previously generated `modules.rst` files because they're automatically generated and changes made to them are overridden. ## Reference to official issue Fixes issue #198. ## Motivation and Context Makes the cases of the `Code Documentation` titles begin with upper case. ## How Has This Been Tested? - `docker-compose -f local.yml build && docker-compose -f local.yml up` - Open [http://localhost:8002/](http://localhost:8002/) - Titles in the section *Code Documention* should start with upper case ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

Closes the issue #203 that threw an error whe you visit the http://localhost:8001/ endpoint in the prediction application. ## Description Using `python -m flask run ...` to start server. More info in docs [here](http://flask.pocoo.org/docs/0.11/cli/#basic-usage) ## Reference to official issue This closes issue #203 ### Steps to reproduce - `docker-compose -f local.yml up` - visit [http://localhost:8001/](http://localhost:8001) - Should load the home page ## Motivation and Context This removes the traceback error when you visit [http://localhost:8001/](http://localhost:8001) ## How Has This Been Tested? When you visit [http://localhost:8001/](http://localhost:8001) you should not get an error ## CLA - [X] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

Hello @ask7 I tried using the `interface` app Dockerfile and I came across some unsuccessful scenarios: When I run: > $ docker-compose -f local.yml up --build compile_docs Everything builds but the container won't finish building because the `interface` app Dockerfile starts the `Django` app and sleeps until a connection to Postgres is established. ```cmd compile_docs_1 | Postgres is unavailable - sleeping compile_docs_1 | Postgres is unavailable - sleeping ``` When I run: > $ docker-compose -f local.yml up Everything builds but I get ```compile_docs_1 | Exception occurred: compile_docs_1 | File "/usr/local/lib/python3.6/site-packages/django/conf/__init__.py", line 39, in _setup compile_docs_1 | % (desc, ENVIRONMENT_VARIABLE)) compile_docs_1 | django.core.exceptions.ImproperlyConfigured: Requested settings, but settings are not configured. You must either define the environment variable DJANGO_SETTINGS_MODULE or call settings.configure() before accessing settings. compile_docs_1 | The full traceback has been saved in /tmp/sphinx-err-0j6r37rq.log, if you want to report the issue to the developers. compile_docs_1 | Please also report this if it was a user error, so that a better error message can be provided next time. compile_docs_1 | A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks! compile_docs_1 | make: *** [html] Error 1 compile_docs_1 | Makefile:29: recipe for target 'html' failed ``` ### current state I am separating the `documentation` docker configs and it's requirements from `interface` app but so far, I am still getting the above error. Do you have any idea on how to set the `DJANGO_SETTINGS_MODULE` during docs compilation? I tried: ```python import os os.envrion['DJANGO_SETTINGS_MODULE'] = 'interface.config.settings...' ``` But that doesn't seem to recognize the `interface` app. I will update when I make progress on this. ### restart: always Since the documentation is done in two separate containers i.e. `compile_docs` which compiles the files into "serveable" html files and `documentation` which renders the files using a simple python server. When you edit a document, it can be synced into the `compile_docs` container through `volumes` but it won't be compiled into a ready html file unless you manually restart the container.

Hi @isms I will definitely have a look. Off the bat I can see that building the container using the `prediction` app requirements is a reason why there are missing packages. Let me try and reproduce on my end then I'll patch this up.

Hi @reubano, I followed your recommendations and finally managed to fix this PR. Kindly check on your end 😀

@reubano let me try this. I will update as soon as I'm done

> Hey @musale, how are you getting on? :) Hi @reubano and @lamby! I've been offline the past few days. I have come to a host of additional commits so I had some challenges rebasing and squashing. I have failing tests for both documentation and prediction. Can you check if it's good to go on your end?

hi @reubano, did you manage to get your docker up and running?

@reubano great! Kindly let me know of any changes that would improve the experience

## Description I have bootstrapped the steps needed for local installation, building and editing of the documentation for this project. ## Reference to official issue This addresses the issue #41 ## Motivation and Context This change enables developers to be able to edit the documentation locally. Since docker is the official development configuration, I used it to create the application and link it to the current development. ## How Has This Been Tested? Locally, when you run `$ docker-compose -f local.yml up` the documentation application will be running on (http://localhost:8002/)[http://localhost:8002/] ## CLA - [x] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

Gotcha @reubano 👍

Hey @reubano will that do?

Hi @reubano I have effected the proposed changes.

## Description I have implemented a githook-pre-commit file that has the `flake8` commands for styling and the command to run tests in the docker containers locally. ## Reference to official issue It meets requirements for #42 ## Motivation and Context This change will allow developers to run flake8 and tests before creating a commit. Flake8 command currently runs on uncommitted and staged python files with changes. This reduces the number of files that will be checked against before a commit. In case of project-wide checks, it could be done at CI level. Documentation on how to set this up locally has also been included. ## How Has This Been Tested? * Remove any existing `pre-commit` files in `.git/hooks` folder i.e. `rm .git/hooks/pre-commit` * Copy the .githooks-pre-commit file into `.git/hooks/` as `pre-commit` * Make it executable using `chmod +x .git/hooks/pre-commit` * Run `.git/hooks/pre-commit` to test the commands * Make a change in the code base, add and commit it. It should run `flake8` and run the tests before committing. If the commands pass, the commit is created otherwise it is not. **Note:** the tests will fail from the current master branch due to #50 . If you patch your code with https://github.com/concept-to-clinic/concept-to-clinic/pull/50 it should pass all tests ## CLA - [x] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well

Fixed a failing test ## Description Initially, the test asserted existence for `Hello` text from the response. This text was not available or of use as of making this PR. The `index.html` template has a constant structure with `<title>Concept to Clinic<\title>` tag text . In addition, serving the `index.html` template should resolve a status 200 OK which is better for checking if the template was loaded. ## Reference to official issue Fixes #7 ## Motivation and Context This will make the tests in the `interface` app pass for `master` branch. ## How Has This Been Tested? In the development setup using docker. Run: `docker-compose -f local.yml run prediction python manage.py test` ## Screenshots (if appropriate): ## CLA - [x] I have signed the CLA; if other committers are in the commit history, they have signed the CLA as well