Merge browser module into master. (#187)

* Browser/fix/open empty annotations (#111)

* Browser/feature/disable page scroll (#116)

* Browser/feature/add canvas padding (#117)

* Update, refactor brush (#120)

* Update browser contrast adjustment (#121)

* Add outline capability to browser (#122)

* Initial timestamp tracking (#124)

* Initial url options, RGB mode (#130)

* Update initial brush params (#136)

* Initial changes to image modification code (#138)

* Fix npz upload issues (#139)

* Misc small changes to rgb (#141)

* Add travis and use Flask Blueprints to remove redundant application files. (#144)

* Add docker-compose.yml for easier local development (#146)

* Change environment variables to AWS standards. (#147)

* fix S3 env vars that got lost in the merge. (#148)

* Update npz canvas (expansion, better scaling, pan+zoom) (#149)

* Update HTML templates with the materialize CSS framework (#154)

* Add logger statements to most backend routes. (#157)

* Use distutils.util.strtobool to cast boolean request args to bools. (#163)

* Fix some browser rgb image generation edge cases (#164)

* Use PIL to create PNGs if not using a cmap. (#165)

* Don't need to return raw data on action requests. (#166)

* Save npzs with X and y (#168)

* Hide labels, bugfixes (#174)

* add flask-cors and enable CORS for all routes. (#178)

* Update browser with better logging and error handling. (#179)

* Add unit tests for Flask application. (#186)

Co-authored-by: geneva-miller <45578681+geneva-miller@users.noreply.github.com>
Co-authored-by: Thomas Dougherty <tdowlingdougherty@gmail.com>

.coveragerc

@@ -0,0 +1,29 @@
+# .coveragerc to control coverage.py
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    except ImportError
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+ignore_errors = True
+# fail_under = 70
+show_missing = True
+
+omit =
+    **/*_test.py
+    env/**/*.py
+    venv/**/*.py
+    ENV/**/*.py
+    VENV/**/*.py
+    desktop/env/**/*.py
+    desktop/venv/**/*.py
+    desktop/ENV/**/*.py
+    desktop/VENV/**/*.py
+    browser/env/**/*.py
+    browser/venv/**/*.py
+    browser/ENV/**/*.py
+    browser/VENV/**/*.py
+    browser/conftest.py

.travis.yml

@@ -0,0 +1,23 @@
+dist: xenial
+
+git:
+  depth: false
+
+language: python
+
+cache: pip
+
+python:
+  - 3.6
+  - 3.7
+  - 3.8
+
+install:
+  - pip install -r browser/requirements.txt
+  - pip install -r browser/requirements-test.txt
+
+script:
+  - pytest browser --cov browser --pep8
+
+after_success:
+  - coveralls

browser/.ebextensions/healthcheckurl.config

@@ -0,0 +1,4 @@
+option_settings:
+  - namespace:  aws:elasticbeanstalk:application
+    option_name:  Application Healthcheck URL
+    value:  /health

browser/.ebextensions/options.config

@@ -1,5 +1,4 @@
 option_settings:
   - namespace: aws:elasticbeanstalk:container:python
     option_name: WSGIPath
-    value: eb_application.py
-
+    value: application.py

browser/.env.example

@@ -0,0 +1,11 @@
+# Flask settings
+DEBUG=
+TEMPLATES_AUTO_RELOAD=
+
+# AWS credentials
+AWS_ACCESS_KEY_ID=
+AWS_SECRET_ACCESS_KEY=
+
+# SQL Alchemy settings
+SQLALCHEMY_DATABASE_URI=
+SQLALCHEMY_TRACK_MODIFICATIONS=

browser/Dockerfile

@@ -0,0 +1,13 @@
+FROM python:3.7
+
+WORKDIR /usr/src/app
+
+COPY requirements.txt requirements.txt
+
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY . .
+
+EXPOSE 5000
+
+CMD ["/bin/sh", "-c", "python application.py"]

browser/README.md

@@ -18,6 +18,32 @@ pip install -r requirements.txt
 ```bash
 python3 application.py
 ```
+## To use docker-compose for local development
+Add your AWS credentials to ```docker-compose.yaml```.
+
+From the ```caliban/browser``` folder, run:
+```bash
+sudo docker-compose up --build -d
+```
+Wait a minute for the database to finish setting up before running:
+```
+sudo docker-compose restart app
+```
+You can now go to 0.0.0.0:5000 in a browser window to access the local version of the tool.
+
+To interact with the local mysql database:
+```
+sudo docker exec -it browser_db_1 bash
+mysql -p
+```
+When finished:
+```
+sudo docker-compose down
+```
+(optional)
+```
+sudo docker system prune --volumes
+```
 
 ## Structure of Browser Version
 
@@ -81,7 +107,7 @@ Keybinds in pixel editing mode are different from those in the label-editing mod
 
 Annotation mode focuses on using an adjustable brush to modify annotations on a pixel level, rather than using operations that apply to every instance of a label within a frame or set of frames. The brush tool will only make changes to the currently selected value. Ie, a brush set to edit cell 5 will only add or erase "5" to the annotated image.
 
-*-/=* - increment value that brush is applying
+*[ (left bracket) / ] (right bracket)* - increment value that brush is applying
 
 *↓ ↑* - change size of brush tool
 
@@ -100,6 +126,10 @@ Annotation mode focuses on using an adjustable brush to modify annotations on a
 
 ### Viewing Options:
 
+*spacebar + click and drag* - pan across canvas
+
+*-/= keys or alt + scroll wheel* - zoom in and out
+
 *c* - cycle between different channels when no cells are selected
 
 *e* - toggle annotation mode (when nothing else selected)